All File Changes

v274_preview2 to v274_base (2012-10-02 to 2012-10-09) v274

• src/hg/hgFileUi/hgFileUi.c
  • lines changed 14, context: html, text, full: html, text
    Add ENCODE log and portal link, for consistency with hgTrackUi
• src/hg/hgGenome/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    adding helpful bolding and a return link to click on.
• src/hg/hgTables/bigBed.c
  • lines changed 9, context: html, text, full: html, text
    If the .bb has no rows for the current chromosome, omit example row display.It would be nicer to just grab the first rows from the bigBed file in this case... don't have time today.
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 27, context: html, text, full: html, text
    Remove preview browser links on ENCODE config pages. #9264. Reuse the slot on menu for ENCODE portal link (long ago plan with Katrina)
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 36, context: html, text, full: html, text
    VCF indel alleles always start with a reference base that is the same(e.g. for a dbSNP item with -/C, the VCF item starts with the reference
    base to the left like A/AC). Make the display consistent with dbSNP
    and other variation tracks by trimming the left neighboring base.
    
  • lines changed 51, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
  • lines changed 52, context: html, text, full: html, text
    Improved mouseover titles for VCF hap-cluster display: trim indel left base,abbreviate long alleles (e.g. 40kb deletion was causing giant mouseover titles
    to be ignored/truncated by web browser).
    
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    changes after code review, #9122
• src/hg/hgc/pubs.c
  • lines changed 28, context: html, text, full: html, text
    adding logos to article pages (preparing for upcoming license change by elsevier)
• src/hg/hgc/vcfClick.c
  • lines changed 193, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 105, context: html, text, full: html, text
    Interim update of Contacts page. Removes encode@soe mailing list and departed staff, highlights & clarifies contact info
• src/hg/htdocs/ENCODE/index.html
  • lines changed 75, context: html, text, full: html, text
    Update News
  • lines changed 71, context: html, text, full: html, text
    Retire old news
  • lines changed 1, context: html, text, full: html, text
    Retire stale New highlight
  • lines changed 17, context: html, text, full: html, text
    Retire links to preview browser. #9264
  • lines changed 1, context: html, text, full: html, text
    Retire preview browser links
  • lines changed 6, context: html, text, full: html, text
    Adding line returns at 100 characters for new news for ENCODE index.html
  • lines changed 1, context: html, text, full: html, text
    Interim update of Contacts page. Removes encode@soe mailing list and departed staff, highlights & clarifies contact info
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 55, context: html, text, full: html, text
    Retire old news
• src/hg/htdocs/ENCODE/search.html
  • lines changed 19, context: html, text, full: html, text
    Retire preview browser links. #9264
• src/hg/htdocs/ENCODE/trackStatus.html
  • lines changed 3, context: html, text, full: html, text
    Retiring encode@soe mailing list
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 1, context: html, text, full: html, text
    Retire old news. Add new OpenHelix tutorial link
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Changing the name file from Identifier of paired-read to The actual peptide sequence, RM#9225
  • lines changed 1, context: html, text, full: html, text
    Changing the name to The peptide sequence, RM#9225
• src/hg/htdocs/images/phylo/mm10_60way.gif
  • lines changed 0, context: html, text, full: html, text
    this one is actually a gif
• src/hg/htdocs/images/phylo/mm10_60way.png
  • lines changed 0, context: html, text, full: html, text
    updated image with phylo group labels
  • lines changed 0, context: html, text, full: html, text
    this one is actually a gif
• src/hg/htdocs/images/pubs_nih.png
  • lines changed 0, context: html, text, full: html, text
    adding logos to article pages (preparing for upcoming license change by elsevier)
• src/hg/htdocs/images/pubs_sciencedirect.png
  • lines changed 0, context: html, text, full: html, text
    adding logos to article pages (preparing for upcoming license change by elsevier)
  • lines changed 0, context: html, text, full: html, text
    elsevier logo change
• src/hg/htdocs/inc/encode.topbar.html
  • lines changed 6, context: html, text, full: html, text
    Remove preview links form ENCODE top menu bars. #9264
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 4, context: html, text, full: html, text
    Remove preview links form ENCODE top menu bars. #9264
• src/hg/htdocs/inc/encodeProjectSoftware.topbar.html
  • lines changed 4, context: html, text, full: html, text
    Remove preview links form ENCODE top menu bars. #9264
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    changes after code review, #9122
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v274
• src/hg/lib/fileUi.c
  • lines changed 9, context: html, text, full: html, text
    Remove links to preview browser. #9264
• src/hg/lib/jksql.c
  • lines changed 10, context: html, text, full: html, text
    changes after code review, #9122
• src/hg/lib/pgSnp.c
  • lines changed 7, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/hg/lib/web.c
  • lines changed 20, context: html, text, full: html, text
    fixing problem with mising PDF/PS link in hgGenome, fixes #9263
  • lines changed 11, context: html, text, full: html, text
    hopefully this is a bit more efficient
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 2, context: html, text, full: html, text
    genbank is reset to gadMor1.refseq.mrna.native.load = no and gadMor1.genbank.mrna.xeno.load = no
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656: GWAS Catalog bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 88, context: html, text, full: html, text
    Track #8886 (Denisova high-coverage): Feedback from data providers:1. Separate "Fixed" subtracks into "Fixed" and "Fixed but in dbSNP".
    2. OK to combine SNCs and InDels to reduce # of subtracks.
    3. OK to hide non-CCDS gene changes, Synonymous, and Reg. Region by default.
    
  • lines changed 6, context: html, text, full: html, text
    Track #1656: GWAS Catalog bi-monthly update.
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 20, context: html, text, full: html, text
    Fixed redmine 8640 note 14 table hg19.ensGene not sorted starting at row 185098: chrM:12337 when doing positionalTblCheck hg19 ensGene problem.
• src/hg/makeDb/doc/mm10Strains1.txt
  • lines changed 352, context: html, text, full: html, text
    done with masking and ready for lastz run
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    experiment to see if genbank.mrna.xeno.load can be yes for a large scaffold assembly
  • lines changed 1, context: html, text, full: html, text
    do not load refseq mrna native on gadMor1
• src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c
  • lines changed 8, context: html, text, full: html, text
    clean up gbSanity to not generate errors that aren't really errors (#8887)
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • lines changed 1, context: html, text, full: html, text
    clean up gbSanity to not generate errors that aren't really errors (#8887)
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added missing assemblies to the section starting on line 105; removed duplicate assemblies from the section starting on line 109 (redmine #8640)
  • lines changed 7, context: html, text, full: html, text
    Fixed redmine #8640 joinerCheck -database=eriEur1 -identifier=ensemblTranscriptId all.joiner -keys Error: 21118 duplicates in eriEur1.ensGene.name including 'ENSEEUT00000000005' problem for 14 db.
  • lines changed 1, context: html, text, full: html, text
    Added myoLuc2 to the section starting on line 105 (redmine #8640)
  • lines changed 9, context: html, text, full: html, text
    redmine 8640 Note #19 Error: 21418 duplicates in dasNov2.ensGene.name fixed.
  • lines changed 4, context: html, text, full: html, text
    Fixed alphabetization (redmine #8640)
  • lines changed 2, context: html, text, full: html, text
    Backout all Chin's change to ignore dup name for ensGeneScaffold check, per agreenment with Steve.
• src/hg/makeDb/trackDb/README
  • lines changed 4, context: html, text, full: html, text
    changes after code review, #9122
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/chimp/panTro2/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Adding validation links for Bernstein pdfs for antibodies H3K9ac and H2A.Z RM#9159 #6
  • lines changed 1, context: html, text, full: html, text
    removing spaces in alpha that Katrina most likely removed from beta earlier, a diff of alpha and beta showed these spaces
  • lines changed 114, context: html, text, full: html, text
    Standardizing vendorNames. Using the model Dr. Blah at Blah for lab generated samples.
  • lines changed 8, context: html, text, full: html, text
    Fixing the Steve Choi Merge Conflict
  • lines changed 51, context: html, text, full: html, text
    Removing _ from the labels
  • lines changed 0, context: html, text, full: html, text
    removing all the double spaces in the terms for consistancy
  • lines changed 16, context: html, text, full: html, text
    Standardizing vendorId for sc biotech numbers and for Missing
  • lines changed 182, context: html, text, full: html, text
    Cleaning up comments, for readablility. Removing excess comments. Removing old commented out stuff.
  • lines changed 4, context: html, text, full: html, text
    Changing typo link from 559 to 599 per RM#9222 comment#5
  • lines changed 21, context: html, text, full: html, text
    Homogenizing term Western_blot, adding six missing validation files 3 human BATF,P300,PBX3, 2 mouse P300, Pol2-4H8
  • lines changed 6, context: html, text, full: html, text
    Staging for moving ripInput from Antibody to Control
  • lines changed 210, context: html, text, full: html, text
    This was a manaul going over to see the type of mistakes I was getting. Things i corrected included, the order of target and targetClass going after antibodyDescription. Adding Antibody Target into the antibodyDescription for the search engine. Correcting target to match the HGNC approved target name. Removing items that did not have validation but were also not used. Trying to make sure that the antibody type like Rabbit monoclonal was at that front of the antibody description. Cleaning up the Missing vendorId for the White lab samples.
  • lines changed 8, context: html, text, full: html, text
    Changing links/term for CV TermID for GM12878 and Dnd41 Cell Lines RM#9282
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 675, context: html, text, full: html, text
    Moving the alpha cv to public
  • lines changed 3, context: html, text, full: html, text
    Copying alpha cv.ra to beta cv.ra adding two documents, removing a i that is not supposed to be in beta.cv, Cricket confirmed
  • lines changed 165, context: html, text, full: html, text
    Copying cv.ra from alpha to beta, changes include removing double spaces, under_score in labels, and correcting vendor name
  • lines changed 202, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, updating link, removing comments, updating vendorID
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 675, context: html, text, full: html, text
    Moving the alpha cv to public
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 27, context: html, text, full: html, text
    Corrected in-text citation, fixed reference, cleaned up html (redmine #8640)
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg18/encodeMsaTbaDec07.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg18/multiz17way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite10.ra
  • lines changed 104, context: html, text, full: html, text
    new patch track for hg19
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
  • lines changed 1, context: html, text, full: html, text
    correct release date on micMur1
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html
  • lines changed 69, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
  • lines changed 5, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Description & label corrections from Fernando Racimo.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 7, context: html, text, full: html, text
    added a '/ul' tag and added some indents to make more readable
  • lines changed 9, context: html, text, full: html, text
    removed some text that sounds too much like advertising
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 11, context: html, text, full: html, text
    added accessions for BroadHistone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 59, context: html, text, full: html, text
    added GEO accessions for a number of tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1128, context: html, text, full: html, text
    added more GEO accessions numbers
  • lines changed 9, context: html, text, full: html, text
    Removing dccAccession
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 266, context: html, text, full: html, text
    added more GEO accessions numbers
  • lines changed 4, context: html, text, full: html, text
    finished accessioning OpenChromDnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 59, context: html, text, full: html, text
    added more GEO accessions numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 176, context: html, text, full: html, text
    added GEO accessions for a number of tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 5, context: html, text, full: html, text
    added GEO accessions for a number of tracks
  • lines changed 21, context: html, text, full: html, text
    additional accessions for UW Histone, finishing the track
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 80, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
  • lines changed 119, context: html, text, full: html, text
    Track #1079 (1000 Genomes Phase 1 Accessible Regions):regions in which short reads map with sufficient mapping quality and enough
    (but not too much) depth to be trustworthy, by two sets of thresholds:
    pilot project and strict. Data & description from Tom Blackwell, UMich.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 421, context: html, text, full: html, text
    Track #8886 (Denisova high-coverage): Feedback from data providers:1. Separate "Fixed" subtracks into "Fixed" and "Fixed but in dbSNP".
    2. OK to combine SNCs and InDels to reduce # of subtracks.
    3. OK to hide non-CCDS gene changes, Synonymous, and Reg. Region by default.
    
  • lines changed 56, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Description & label corrections from Fernando Racimo.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    Track #1079 (1000 Genomes Phase 1 Accessible Regions):regions in which short reads map with sufficient mapping quality and enough
    (but not too much) depth to be trustworthy, by two sets of thresholds:
    pilot project and strict. Data & description from Tom Blackwell, UMich.
    
  • lines changed 7, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
  • lines changed 4, context: html, text, full: html, text
    proper alpha beta public tags on the altSeqSomposite tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 45, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/max.larryPop.trackDb.ra
  • lines changed 106, context: html, text, full: html, text
    cleaning up trackDb dir, removing accidentally checked in trackDb files
• src/hg/makeDb/trackDb/max.pubDens.trackDb.ra
  • lines changed 252, context: html, text, full: html, text
    cleaning up trackDb dir, removing accidentally checked in trackDb files
• src/hg/makeDb/trackDb/max.trackDb.ra
  • lines changed 68, context: html, text, full: html, text
    cleaning up trackDb dir, removing accidentally checked in trackDb files
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 8, context: html, text, full: html, text
    Punctuation and capitalization changes to table 1. Thanks, Greg.
  • lines changed 1, context: html, text, full: html, text
    remove the Chinese from Rhesus
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
  • lines changed 4, context: html, text, full: html, text
    Removed link to phyloP vertebrate subset tree model, which no longer exists.
  • lines changed 1, context: html, text, full: html, text
    Removed 'as of March 2007' from statement about what the phylogenetic tree is based on.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 1, context: html, text, full: html, text
    change mm10_60way image to gif
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 493, context: html, text, full: html, text
    added GEO accessions for a number of tracks
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/quality.html
  • lines changed 5, context: html, text, full: html, text
    Removed range for scores, and guidelines for intepreting scores, as there is no single standard for meanings of quality scores. See http://redmine.soe.ucsc.edu/issues/7681#note-7.
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed displays from squish to dense per code review.
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 2, context: html, text, full: html, text
    Removed claim that repeats are shown in lower-case in hgTracks, per http://redmine.soe.ucsc.edu/issues/7038#note-102.
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 1, context: html, text, full: html, text
    took out crypt.h it's not needed and breaks the compile on MacOs. #8746
• src/hg/txGene/txGeneExplainUpdate2/txGeneExplainUpdate2.c
  • lines changed 45, context: html, text, full: html, text
    output a set of codes to explain the change of a gene model, rather than a single note. #7045
• src/hg/utils/decipher/buildDecipher
  • lines changed 19, context: html, text, full: html, text
    add validation to DECIPHER table loading. Now it'll fail if any of the four tables has changed more than 10% (#8840)
• src/hg/utils/decipher/checkDecipher.sh
  • lines changed 11, context: html, text, full: html, text
    add validation to DECIPHER table loading. Now it'll fail if any of the four tables has changed more than 10% (#8840)
• src/hg/utils/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    add validation to DECIPHER table loading. Now it'll fail if any of the four tables has changed more than 10% (#8840)
• src/hg/utils/decipher/validateDecipher.sh
  • lines changed 30, context: html, text, full: html, text
    add validation to DECIPHER table loading. Now it'll fail if any of the four tables has changed more than 10% (#8840)
• src/inc/vcf.h
  • lines changed 3, context: html, text, full: html, text
    Expose vcfFilePooledStr to callers (for example to share allele storage).
  • lines changed 9, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Bug #9265 (bigBed with columns containing spaces is mangled in hgTables schema and output):chop by tabs, not spaces, in bigBedIntervalToRow. bedToBigBed always stores tab-sep.
    
• src/lib/vcf.c
  • lines changed 5, context: html, text, full: html, text
    Expose vcfFilePooledStr to callers (for example to share allele storage).
  • lines changed 37, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/parasol/inc/paraVersion.h
  • lines changed 1, context: html, text, full: html, text
    adding flushResults to para and parasol clients
• src/parasol/para/para.c
  • lines changed 37, context: html, text, full: html, text
    adding flushResults to para and parasol clients
• src/parasol/paraHub/paraHub.c
  • lines changed 44, context: html, text, full: html, text
    adding flushResults to para and parasol clients
• src/parasol/parasol/parasol.c
  • lines changed 42, context: html, text, full: html, text
    adding flushResults to para and parasol clients
• src/parasol/version.doc
  • lines changed 2, context: html, text, full: html, text
    adding flushResults to para and parasol clients
• src/utils/bbTest/makefile
  • lines changed 1, context: html, text, full: html, text
    Use "L += ..." instead of "L = ..." to avoid losing inc/common.mk $USE_* tweaks.
• src/utils/qa/findOrg.csh
  • lines changed 8, context: html, text, full: html, text
    Changed requirement to run on hgwdev to capability to run on either hgwdev or hgwbeta.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v274 final build
• src/utils/qa/weeklybld/summaryEmail.sh
  • lines changed 1, context: html, text, full: html, text
    v274 final build

• lines changed: 7800
• files changed: 190