All File Changes

v303_preview to v303_preview2 (2014-07-07 to 2014-07-14) v303

• src/hg/altSplice/altSplice/sequenceForBed.c
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in option name preventing upCase from working
• src/hg/expData/expData.c
  • lines changed 104, context: html, text, full: html, text
    A program that runs on SQL data. Re organizes the data into tissue specific rows for differential expression analysis
  • lines changed 117, context: html, text, full: html, text
    Modified significantly. Takes in a processed table of expression data, and outputs a file with comparison data
  • lines changed 190, context: html, text, full: html, text
    Takes in input files and performs an expression analysis using a Hac Tree. The output file is a binary tree, each leaf node is a specific tissue.
  • lines changed 93, context: html, text, full: html, text
    The program now prints out files in Json format
  • lines changed 45, context: html, text, full: html, text
    Added new comments, json output is still not working
• src/hg/hgConvert/hgConvert.c
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    hgConvert was missing a call to setUdcCacheDir, so it was using the default /tmp/udcCache/.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 7, context: html, text, full: html, text
    add Malacards link out of hgGene
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 59, context: html, text, full: html, text
    put "retry hub" button with error message so folks can disconnect frompublic hubs with errors
    
• src/hg/hgSession/hgSession.c
  • lines changed 7, context: html, text, full: html, text
    fix a couple of problems with assembly hubs and sessions. #13078 #13587
• src/hg/hgTracks/vcfTrack.c
  • lines changed 21, context: html, text, full: html, text
    Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
    or apply minimum QUAL score / minimum minor allele frequency filters.
    
• src/hg/hgVai/hgVai.c
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    Moved Regulatory annotations out of 'Select More Annotations' into theirown top-level section because they are not just another annotation source --
    they cause us to assign a specific consequence type. Also, as Jonathan suggested,
    I'm suppressing regulatory annotation info for gene-consequence lines of outputs.
    That makes the output a lot less redundant while still providing details for
    RegulatoryFeature lines of output.
    
  • lines changed 19, context: html, text, full: html, text
    Added COSMIC as an optional annotation. refs #11228
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 43, context: html, text, full: html, text
    Wording corrections, updates, and additions to the GBiB help docs, refs #12843
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 21, context: html, text, full: html, text
    Added Farrell pub. Updated PMC links for a few citations.
  • lines changed 2, context: html, text, full: html, text
    Fixed typo in Kristensen citation -- line break in html caused incorrect display of special character.
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    added current protocols paper written with OpenHelix
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    oops. added back Miga ref accidentally deleted
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 3, context: html, text, full: html, text
    Fixes #13555. Some links were not relative in globalNavBar.inc
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
    or apply minimum QUAL score / minimum minor allele frequency filters.
    
• src/hg/lib/annoFormatVep.c
  • lines changed 4, context: html, text, full: html, text
    Moved Regulatory annotations out of 'Select More Annotations' into theirown top-level section because they are not just another annotation source --
    they cause us to assign a specific consequence type. Also, as Jonathan suggested,
    I'm suppressing regulatory annotation info for gene-consequence lines of outputs.
    That makes the output a lot less redundant while still providing details for
    RegulatoryFeature lines of output.
    
• src/hg/lib/cart.c
  • lines changed 14, context: html, text, full: html, text
    fix a couple of problems with assembly hubs and sessions. #13078 #13587
  • lines changed 10, context: html, text, full: html, text
    Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
    or apply minimum QUAL score / minimum minor allele frequency filters.
    
• src/hg/lib/vcfUi.c
  • lines changed 14, context: html, text, full: html, text
    Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
    or apply minimum QUAL score / minimum minor allele frequency filters.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    Rebuilt LRG in hg19 and hg38 with corrected URLs for some sources whoseURLs have changed; eventually I expect these to be fixed in LRG xml.
    
• src/hg/makeDb/doc/hg38.txt
  • lines changed 14, context: html, text, full: html, text
    Rebuilt LRG in hg19 and hg38 with corrected URLs for some sources whoseURLs have changed; eventually I expect these to be fixed in LRG xml.
    
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 49, context: html, text, full: html, text
    set up search rule for gold/assembly track refs #9347
• src/hg/makeDb/doc/rn6.txt
  • lines changed 661, context: html, text, full: html, text
    building rn6 refs #13578
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    ready for genbank run refs #13578
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 49, context: html, text, full: html, text
    add search rule for gold/assembly track refs #9348
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added rn6 refs #13578
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding rn6 rat refs #13578
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Added ochPri3 (redmine #9347)
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added rn6 refs #13578
  • lines changed 2, context: html, text, full: html, text
    Moved ochPri2 to secondary assembly list (redmine #9347)
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    need more Sorex/shrew names to match a larger and yet still miniscule set, refs #9348
• src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on alpaca (vicPac1) track description pages
• src/hg/makeDb/trackDb/alpaca/vicPac1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on alpaca (vicPac1) track description pages
• src/hg/makeDb/trackDb/alpaca/vicPac1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on alpaca (vicPac1) track description pages
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 53, context: html, text, full: html, text
    Changing links on medium ground finch (geoFor1) track description
• src/hg/makeDb/trackDb/birds/geoFor1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on medium ground finch (geoFor1) track description
• src/hg/makeDb/trackDb/birds/geoFor1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on medium ground finch (geoFor1) track description
• src/hg/makeDb/trackDb/birds/geoFor1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on medium ground finch (geoFor1) track description
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 6, context: html, text, full: html, text
    Changing links on cow (bosTau6) and lizard (anoCar1) gateway description pages
• src/hg/makeDb/trackDb/drosophila/dp3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosophila (dp3 and droVir1) track description pages
• src/hg/makeDb/trackDb/drosophila/dp3/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosophila (dp3 and droVir1) track description pages
• src/hg/makeDb/trackDb/drosophila/dp3/genewise.html
  • lines changed 13, context: html, text, full: html, text
    Changing links on drosophila (dp3 and droVir1) track description pages
• src/hg/makeDb/trackDb/drosophila/dp3/twinscan.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on drosophila (dp3 and droVir1) track description pages
• src/hg/makeDb/trackDb/drosophila/droVir1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosophila (dp3 and droVir1) track description pages
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 25, context: html, text, full: html, text
    Changing links on fugu (fr3) track description pages
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on fugu (fr3) track description pages
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 52, context: html, text, full: html, text
    Changing links on gorilla (gorGor3) track description pages
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on gorilla (gorGor3) track description pages
• src/hg/makeDb/trackDb/gorilla/gorGor3/gap.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on gorilla (gorGor3) track description pages
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on guinea pig (cavPor3) track description pages
• src/hg/makeDb/trackDb/guineaPig/cavPor3/nscanGene.html
  • lines changed 42, context: html, text, full: html, text
    Changing links on guinea pig (cavPor3) track description pages
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 12, context: html, text, full: html, text
    Made changes to add new chain/net tracks and display proper values (redmine #9347,9348)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changing link tokens to be new item start/end ones added by Tim. refs #13218
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 3, context: html, text, full: html, text
    Making html changes to Segmentation track Code Review #13573
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 54, context: html, text, full: html, text
    Added track entry for Retroposed Genes version 8.
  • lines changed 2, context: html, text, full: html, text
    Changed visibility to hide and removed nextItem on by default.
• src/hg/makeDb/trackDb/lizard/anoCar1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on cow (bosTau6) and lizard (anoCar1) gateway description pages
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    rn6 build underway refs #13578
• src/hg/makeDb/trackDb/marmoset/calJac3/bacEnds.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on marmoset (calJac3) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on marmoset (calJac3) track description pages
• src/hg/makeDb/trackDb/medaka/oryLat2/ctgPos2.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on medaka (oryLat2) track description pages
• src/hg/makeDb/trackDb/medaka/oryLat2/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on medaka (oryLat2) track description pages
• src/hg/makeDb/trackDb/medaka/oryLat2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on medaka (oryLat2) track description pages
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 74, context: html, text, full: html, text
    Changing links on medaka (oryLat2) track description pages
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
  • lines changed 42, context: html, text, full: html, text
    Changing links on medaka (oryLat2) track description pages
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes to add new chain/net tracks and display proper values (redmine #9347,9348)
• src/hg/makeDb/trackDb/opossum/monDom4/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on opossum (monDom4) track description pages
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 81, context: html, text, full: html, text
    Changing links on opossum (monDom4) track description pages
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
  • lines changed 50, context: html, text, full: html, text
    Changing links on opossum (monDom4) track description pages
• src/hg/makeDb/trackDb/pika/ochPri3/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor corrections (redmine #9347,9348)
• src/hg/makeDb/trackDb/pika/ochPri3/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #9347,9348)
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    add search rule for gold/assembly track refs #9347
  • lines changed 1, context: html, text, full: html, text
    Made changes to add new chain/net tracks and display proper values (redmine #9347,9348)
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Added missing target=_blank to external link.
  • lines changed 3, context: html, text, full: html, text
    Added several missing target=_blank to external links.
• src/hg/makeDb/trackDb/rat/affyRAE230.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/rat/affyU34A.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/rat/gnfAtlas2.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/rat/rn3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/rat/rn6/description.html
  • lines changed 63, context: html, text, full: html, text
    rn6 build underway refs #13578
• src/hg/makeDb/trackDb/rat/rn6/gap.html
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    rn6 build underway refs #13578
• src/hg/makeDb/trackDb/rat/rn6/gold.html
  • lines changed 37, context: html, text, full: html, text
    rn6 build underway refs #13578
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    rn6 build underway refs #13578
• src/hg/makeDb/trackDb/rat/stsMapRat.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/shrew/sorAra2/description.html
  • lines changed 2, context: html, text, full: html, text
    Fixed assembly link (redmine #9348)
• src/hg/makeDb/trackDb/shrew/sorAra2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor corrections (redmine #9347,9348)
• src/hg/makeDb/trackDb/shrew/sorAra2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #9347,9348)
• src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    add search rule for gold/assembly track refs #9348
  • lines changed 3, context: html, text, full: html, text
    Made changes to add new chain/net tracks and display proper values (redmine #9347,9348)
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    Set human chain/net default visibility to pack (redmine #9348)
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 7, context: html, text, full: html, text
    Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
    or apply minimum QUAL score / minimum minor allele frequency filters.
    
• src/hg/makeDb/trackDb/xenTro/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on xenTro1 track description pages
• src/hg/makeDb/trackDb/xenTro/xenTro1/description.html
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    Changing links on xenTro1 track description pages
• src/hg/makeDb/trackDb/zebrafish/affyZebrafish.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/affyZonWildType.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainSelf.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/ctgPos2.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/description.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/gold.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
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    Changing links on zebrafish (danRer3) track description pages
• src/hg/utils/automation/parseLrgXml.pl
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    I had assumed that each LRG would have a single source, but that wasincorrect; both names and urls were being concatenated. Since hgc
    expects a single name and url, for now I'll just pick the first
    non-empty name/url (there are sources with no names, just a contact
    entry). After this LRG release, I can update hgc to handle comma-sep
    names and urls. Then, next LRG release, this should be updated to
    make comma-sep names and urls.
    
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
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    make the list of databases supported by a public hub reflect theordering of them in the genomes.txt file
    
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 1, context: html, text, full: html, text
    Fix typo in comment.
• src/utils/bamMerge/bamMerge.c
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    Updated the main for loop to be 0 based index rather than 1 based index
• src/utils/bamSplitByChrom/bamSplitByChrom.c
  • lines changed 1, context: html, text, full: html, text
    Changed comments to be more informative
• src/utils/qa/copyHgcentral
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    Enabled beta -> rr copying (redmine #6508)
• src/utils/qa/weeklybld/buildEnv.csh
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    v303 preview1 refs #13448
  • lines changed 2, context: html, text, full: html, text
    v303 preview2 refs #13448

• lines changed: 2878
• files changed: 116