All File Changes

v246_preview2 to v246_base (2011-01-18 to 2011-01-25) v246

• python/ucscGenomics/__init__.py
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    Added style guide
• python/ucscGenomics/styleGuide.txt
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    Added style guide
• python/ucscgenomics/__init__.py
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    Added style guide
• python/ucscgenomics/rafile/.read.py.swp
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    added rafile python scripts
• python/ucscgenomics/rafile/__init__.py
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    added rafile python scripts
• python/ucscgenomics/rafile/radict.py
  • lines changed 63, context: html, text, full: html, text
    added rafile python scripts
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    updated ra scripts
• python/ucscgenomics/rafile/radict.pyc
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    added rafile python scripts
• python/ucscgenomics/rafile/read.py
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    added rafile python scripts
  • lines changed 33, context: html, text, full: html, text
    added initial test script for rafile read
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    updated ra scripts
• python/ucscgenomics/rafile/test.py
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    added initial test script for rafile read
• python/ucscgenomics/rafile/testinput
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    added rafile python scripts
  • lines changed 8, context: html, text, full: html, text
    added initial test script for rafile read
• python/ucscgenomics/rafile/write.py
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    added rafile python scripts
• python/ucscgenomics/style.txt
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    Added style guide
• src/hg/altSplice/altSplice/genePredToPsl.c
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    genePredToPsl.c
• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
  • lines changed 47, context: html, text, full: html, text
    Adding DAF modifications that came up during freeze submissions
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Adding DAF modifications that came up during freeze submissions
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
  • lines changed 15, context: html, text, full: html, text
    Adding DAF modifications that came up during freeze submissions
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • lines changed 1, context: html, text, full: html, text
    Adding DAF modifications that came up during freeze submissions
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
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    Adding DAF modifications that came up during freeze submissions
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
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    Updated BAM validation to look for 99.9% of file that agrese with 3 mismatches.
• src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
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    Fixed DAF so that Peaks and Signal will not be required for all experiments. Inputs generate ALignments and Raw Data only and are subtracted from experiments with antibodies to generate Peaks and Signals.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
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    added support for bed (and not just bed\d+) and bedLogR
• src/hg/encode/encodeMkChangeNotes/makefile
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    removed install target that puts encodeMkChangeNotes in the pipeline bin directory
• src/hg/encode/encodeValidate/config/fields.ra
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    added terms that are already in CV, not sure why they need to be here as well, but the validator kept complaining
• src/hg/encode/encodeValidate/doEncodeValidate.pl
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    Fixed coding style to conform to camelCase of new subroutine. Also added whitespace after my decleration.
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.hg18.soft
  • lines changed 1712, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.soft
  • lines changed 1712, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg18.soft
  • lines changed 339, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.soft
  • lines changed 339, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.hg18.soft
  • lines changed 4436, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.soft
  • lines changed 4436, context: html, text, full: html, text
    renamed SOFT files to have assembly
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • lines changed 1, context: html, text, full: html, text
    fixing problem with invalid URLs with no "protocol://site/" in url, and also fixed the problem with the display of the paraFetch status as it progresses.
  • lines changed 9, context: html, text, full: html, text
    checking earlier for the right URL protocol will help users catch problems earlier
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 10, context: html, text, full: html, text
    fixing problem with invalid URLs with no "protocol://site/" in url, and also fixed the problem with the display of the paraFetch status as it progresses.
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • lines changed 3, context: html, text, full: html, text
    fixing problem with invalid URLs with no "protocol://site/" in url, and also fixed the problem with the display of the paraFetch status as it progresses.
• src/hg/encode/validateFiles/validateFiles.c
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    add a missing newline in the usage statement
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    fix bug where reporting caused bad abort messages
• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 4, context: html, text, full: html, text
    fixed typos in help message and made it more detailed
• src/hg/hgApi/hgApi.c
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    Only need to get tdb and ancestors when populating '...' metadata.
• src/hg/hgCustom/hgCustom.c
  • lines changed 3, context: html, text, full: html, text
    The call here to customTracksSaveCart seems superfluous and causes errors in updating the html doc
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    Revert "The call here to customTracksSaveCart seems superfluous and causes errors in updating the html doc" This reverts commit fed02927c85bea25c3dc5117590aa8d46e39da72.
• src/hg/hgTables/bigBed.c
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    Fixed bug with bigBed in table browser.
• src/hg/hgTables/bigWig.c
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    Fixing memory allocation problem where one path through the code was not allocating return value dynamically, causing trouble when it was later freed.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    Fixing gross abuse of hTrackDb (via hTrackDbForTrack) found by Larryand Hiram during work on Bug #1114: snp125OfferGeneTracksForFunction was modifying the returned results, which broke when caching was introduced to hTrackDb. Since hgTrackUi already has trackHash, just look up tdbs there and do a shallow copy so that altering the next pointer with slAddHead and slSort doesn't destroy the cached version.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 15, context: html, text, full: html, text
    Moving a bbiFile processing routine from hgTracks to library, so hgc could use it too. Using it to make hgc on bigBed work better.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 91, context: html, text, full: html, text
    some stubs to support ENCODE GIS Chia-pet track
• src/hg/hgc/bigBedClick.c
  • lines changed 5, context: html, text, full: html, text
    Moving a bbiFile processing routine from hgTracks to library, so hgc could use it too. Using it to make hgc on bigBed work better.
• src/hg/hgc/hgc.c
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    add click handler for interactions
• src/hg/htdocs/ENCODE/aboutScaleup.html
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    Make restrictions timestamps more obvious and data policy clearer (input from ENCODE PI's, Tim Hubbard) for ENCODE101.
  • lines changed 9, context: html, text, full: html, text
    Add 'click to enlarge' for graphic, and also credits
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 26, context: html, text, full: html, text
    Make restrictions timestamps more obvious and data policy clearer (input from ENCODE PI's, Tim Hubbard) for ENCODE101.
  • lines changed 15, context: html, text, full: html, text
    Made a few minor edits.
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 26, context: html, text, full: html, text
    Make restrictions timestamps more obvious and data policy clearer (input from ENCODE PI's, Tim Hubbard) for ENCODE101.
  • lines changed 15, context: html, text, full: html, text
    Made a few minor edits.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 4, context: html, text, full: html, text
    Make restrictions timestamps more obvious and data policy clearer (input from ENCODE PI's, Tim Hubbard) for ENCODE101.
  • lines changed 4, context: html, text, full: html, text
    Add 'click to enlarge' for graphic, and also credits
  • lines changed 17, context: html, text, full: html, text
    Made a few minor edits.
• src/hg/htdocs/ENCODE/terms.html
  • lines changed 6, context: html, text, full: html, text
    Make restrictions timestamps more obvious and data policy clearer (input from ENCODE PI's, Tim Hubbard) for ENCODE101.
  • lines changed 25, context: html, text, full: html, text
    Made a few minor edits.
• src/hg/htdocs/FAQ/FAQformat.html
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    cleaning up the wording and adding link to real source code definition for twoBit (all approved by Hiram)
• src/hg/htdocs/Neandertal/index.html
  • lines changed 5, context: html, text, full: html, text
    adding info about remapping to hg19
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    verb tense
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    Added Brian to danRer7 credits.
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    added explicit mention of https to make it easier to find
• src/hg/htdocs/images/EncodeNatureGraphic.png
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    Graphic from ENCODE Pilot Nature paper
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    Add 'click to enlarge' for graphic, and also credits
• src/hg/htdocs/images/floretPreview.jpg
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    A cut at background for preview server
• src/hg/htdocs/images/phylo/danRer7_8way.png
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    updated tree image for danRer7 8-way
• src/hg/htdocs/indexNews.html
  • lines changed 57, context: html, text, full: html, text
    Added announcement about danRer7 browser.
  • lines changed 6, context: html, text, full: html, text
    Fixed broken link.
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    Removed coverage info from danRer7 announcement -- I think this was a carryover from the previous release, and I don't see info from Sanger backing up this number.
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    adding comma and updating link to Sanger guidelines/legal since Sanger was redirecting old link
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    Moving a bbiFile processing routine from hgTracks to library, so hgc could use it too. Using it to make hgc on bigBed work better.
• src/hg/inc/versionInfo.h
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    New version number v246
• src/hg/js/hgTracks.js
  • lines changed 32, context: html, text, full: html, text
    don't add chrom to wikiTrack links (see redmine #2476); fix cases where didn't show both 'Open details...' and 'Show details...' menu items
• src/hg/lib/customFactory.c
  • lines changed 9, context: html, text, full: html, text
    one incorrect memory leak free and only need to read one byte to test file exists and update access time
  • lines changed 10, context: html, text, full: html, text
    I saw the readAndIgnore actually fail after opening the file. No need to fail this business
  • lines changed 1, context: html, text, full: html, text
    fixing bugs with handling of htmlFile; and bouncing unacceptable changes rather than saving them even when they are bad
• src/hg/lib/customTrack.c
  • lines changed 12, context: html, text, full: html, text
    fixing a bug with chewed up original input, and added checking for problems caused by users accidentally pasting ct data into the html documentation field
  • lines changed 3, context: html, text, full: html, text
    fixing bugs with handling of htmlFile; and bouncing unacceptable changes rather than saving them even when they are bad
• src/hg/lib/hdb.c
  • lines changed 15, context: html, text, full: html, text
    Moving a bbiFile processing routine from hgTracks to library, so hgc could use it too. Using it to make hgc on bigBed work better.
  • lines changed 11, context: html, text, full: html, text
    Needed to hook up generations and set container flags when getting tdb for track and ancestors
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 2040 note 17. Some track lists would not respond properly to List subtracks selected v. all radio button.
  • lines changed 5, context: html, text, full: html, text
    Fix for redmine 2520. Downloads link for individual file was broken by hgFileUi logic.
• src/hg/lib/omimDisorderMap.sql
  • lines changed 9, context: html, text, full: html, text
    Created omimDisorderMap.sql for OMIM subtracks build pipeline.
• src/hg/lib/omimDisorderPhenotype.sql
  • lines changed 12, context: html, text, full: html, text
    Created omimDisorderPhenotype.sql for OMIM related subtracks build pipeline.
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 216, context: html, text, full: html, text
    8-way alignments all redone with new fish phylo tree
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 731, context: html, text, full: html, text
    Broad in pushQ. Forgot to check this doc in earlier
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 461, context: html, text, full: html, text
    New submissions and a new composite: wgEncodeOpenChromSynth
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release1.notes
  • lines changed 772, context: html, text, full: html, text
    Updated notes file with the signals only version Jim requested
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release1.notes
  • lines changed 254, context: html, text, full: html, text
    added the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release1.notes
  • lines changed 69, context: html, text, full: html, text
    Modified notes to include new files
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 36, context: html, text, full: html, text
    Phylogenetic tree from 6-way
  • lines changed 38, context: html, text, full: html, text
    re-run Phylogenetic tree using phast.2010-12-30
  • lines changed 276, context: html, text, full: html, text
    phastCons for felCat4
  • lines changed 170, context: html, text, full: html, text
    phyloP for 6-way felCat4
• src/hg/makeDb/doc/hg19.txt
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    Added stuff for making the bedGraph file ok.
  • lines changed 6, context: html, text, full: html, text
    Fixing the problem with the Fosmid Pairs track with clicks on an alignment.
  • lines changed 8, context: html, text, full: html, text
    Changed table-copying technique because indexes in the hg18 tables were not preserved in the copy. This way they are.
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    Changed table-copy method from hg18 so indexes are preserved.
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    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 59, context: html, text, full: html, text
    Progressed in the script, added some testing ideas as comments
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    added species change
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    adding danRer7 to the genbank updates
• src/hg/makeDb/genbank/src/rtdb/README
  • lines changed 196, context: html, text, full: html, text
    removed dead-end project that was never completed
• src/hg/makeDb/genbank/src/rtdb/rtdbServer/makefile
  • lines changed 13, context: html, text, full: html, text
    removed dead-end project that was never completed
• src/hg/makeDb/genbank/src/rtdb/rtdbServer/rtdbServer.c
  • lines changed 328, context: html, text, full: html, text
    removed dead-end project that was never completed
• src/hg/makeDb/genbank/src/rtdb/rtdbUpdate
  • lines changed 239, context: html, text, full: html, text
    removed dead-end project that was never completed
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    redmine #1485 ignored poly(A) tables
• src/hg/makeDb/trackDb/README
  • lines changed 26, context: html, text, full: html, text
    Add info about fileSortOrder and hgFileUi for composites
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Added treatment for Crawford
  • lines changed 6, context: html, text, full: html, text
    Added Rip-seq
  • lines changed 28, context: html, text, full: html, text
    Added two new antibodies and one antibody validation document. I'd tried before, but messed up with git stash
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    Corrected a bug where two antibodies had vendors but not vendorIds
  • lines changed 2, context: html, text, full: html, text
    Once more, trying to fix a bug where an antibody has a vendor but not vendor ID
  • lines changed 2, context: html, text, full: html, text
    trying one more time to get this antibody thing cleared up...
  • lines changed 8, context: html, text, full: html, text
    Added shortPolyA for rnaExtract for HAIB
  • lines changed 16, context: html, text, full: html, text
    added BioChain as a lab and a new mapAlgorithm
  • lines changed 24, context: html, text, full: html, text
    Adding two new treatments for the Myers lab
  • lines changed 5, context: html, text, full: html, text
    Accepted several provisional changes
  • lines changed 17, context: html, text, full: html, text
    some Gis Chia Pet changes
  • lines changed 2, context: html, text, full: html, text
    Fixed miss spelling of Provisional
  • lines changed 5, context: html, text, full: html, text
    Added new dataType Nucelosome.
  • lines changed 7, context: html, text, full: html, text
    Accepted several provisional stanzas
  • lines changed 75, context: html, text, full: html, text
    Added several new antibodies for the White lab
  • lines changed 5, context: html, text, full: html, text
    When adding the White lab antibodies, forgot to add a placeholder for vendor ID
  • lines changed 3, context: html, text, full: html, text
    fixed duplications in cv.ra
  • lines changed 15, context: html, text, full: html, text
    Added new antibody for White lab: eGFP-NR4A1
  • lines changed 119, context: html, text, full: html, text
    Added 8 antibodies for Myers lab that did not have validation documents.
  • lines changed 6, context: html, text, full: html, text
    Added new Seq Platform AB SOLiD 3 Plus
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    Added new Control Terms for controls used when comparing for a specific antibody replicate. Lab doesn't use 1 run of a control to compare all results, but rather a control is run at the same time for each antibody specific experiment.
  • lines changed 69, context: html, text, full: html, text
    Accepted several provisional stanzas
  • lines changed 5, context: html, text, full: html, text
    Added comments for a provisional stanza
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 819, context: html, text, full: html, text
    Moving a bundle of changes from alpha to beta
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 2, context: html, text, full: html, text
    busted by Greg during code review for not getting the citation correct!
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to IMCB
• src/hg/makeDb/trackDb/human/agilentCghAlpha.html
  • lines changed 16, context: html, text, full: html, text
    adding bit about how track was colored along with fixing the count(*) so that they are accurate
• src/hg/makeDb/trackDb/human/hapmapLdPh.html
  • lines changed 175, context: html, text, full: html, text
    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
• src/hg/makeDb/trackDb/human/hg18/hapmapLdPh.html
  • lines changed 175, context: html, text, full: html, text
    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Needed to add Broad HMM
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 154, context: html, text, full: html, text
    Initial submission of wgEncodeBroadHmm composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 16, context: html, text, full: html, text
    staging GEO acc in metaDb on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 16, context: html, text, full: html, text
    releasing GEO accession additions
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Initial submission of wgEncodeBroadHmm composite
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 106, context: html, text, full: html, text
    Initial submission of wgEncodeBroadHmm composite
• src/hg/makeDb/trackDb/human/hg19/gad.html
  • lines changed 95, context: html, text, full: html, text
    Removed a link in the hg19 version of the description that auto-loaded an hg18 custom track on hg19 which caused an error.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Added the .ra file for the UNC / BSU proteogenomics track
  • lines changed 1, context: html, text, full: html, text
    Needed to add Open Chromating Synthesis track
  • lines changed 1, context: html, text, full: html, text
    added new composite HaibGenotype (CNV), created a new trackDb, added line to trackDb.wgEncode, added a new metaDb/alpha file, added a line to the makefile, added the bedLogR type to tagTypes.tab
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    added the composite HAIB RNA-seq. The metaData is loaded, but the tracks are not
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 155, context: html, text, full: html, text
    added two more experiments and fixed the on/off defaults
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 4928, context: html, text, full: html, text
    added 56 new experiments for CSHLShort Release 2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 106, context: html, text, full: html, text
    changed the subID 3081 to the corrected number 3200
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 187, context: html, text, full: html, text
    Added 2 new experiments
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 1786, context: html, text, full: html, text
    added new composite HaibGenotype (CNV), created a new trackDb, added line to trackDb.wgEncode, added a new metaDb/alpha file, added a line to the makefile, added the bedLogR type to tagTypes.tab
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 39, context: html, text, full: html, text
    added 2 more experiments
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 2821, context: html, text, full: html, text
    added the composite HAIB RNA-seq. The metaData is loaded, but the tracks are not
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1706, context: html, text, full: html, text
    Added 10 Chip-seq submissions for the Jan 2011 freeze.
  • lines changed 564, context: html, text, full: html, text
    Added 4 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 9, context: html, text, full: html, text
    ChromChip update
  • lines changed 196, context: html, text, full: html, text
    New submissions
  • lines changed 405, context: html, text, full: html, text
    Fixed controlId and setType. There may still need to be a few controlId changes yet
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 312, context: html, text, full: html, text
    Fixed controlId and setType. There may still need to be a few controlId changes yet
  • lines changed 24, context: html, text, full: html, text
    Fixed some gender issues
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 3, context: html, text, full: html, text
    OpenChromFaire update
  • lines changed 483, context: html, text, full: html, text
    New submissions
  • lines changed 174, context: html, text, full: html, text
    Fixed controlId and setType. There may still need to be a few controlId changes yet
  • lines changed 118, context: html, text, full: html, text
    Addition of last submission for freeze
  • lines changed 8, context: html, text, full: html, text
    Update controlId for just added A549
  • lines changed 16, context: html, text, full: html, text
    Fixed some gender issues
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 127, context: html, text, full: html, text
    Initial checkin of Open Chom Synthesis tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 475, context: html, text, full: html, text
    added 10 more experiments
  • lines changed 265, context: html, text, full: html, text
    Added signals to the second release, this caused many issues as they used to be called clusters
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3389, context: html, text, full: html, text
    Added 29 submissions for the Jan 2011 Freeze. Also, removed commented lines out of trackDb and reorder treatment and antibodies in alphabetical order.
  • lines changed 7, context: html, text, full: html, text
    Fixed controlId's for obj that had HeLaS3/None/Input/IgG-rab where cell line was miss spelled.
  • lines changed 641, context: html, text, full: html, text
    Added 5 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 39, context: html, text, full: html, text
    Adding the metadata for the UNC/BSU Proteogenomics track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 52, context: html, text, full: html, text
    renamed 3 fastqs in UwDnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 35, context: html, text, full: html, text
    renamed 2 fastqs in YaleRnaSeq
  • lines changed 3, context: html, text, full: html, text
    fixed treatment tag in YaleRna
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata on beta for UW Histone hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 18024, context: html, text, full: html, text
    staging metadata on beta for UW Histone hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    added 56 new experiments for CSHLShort Release 2
  • lines changed 1, context: html, text, full: html, text
    Initial checkin of Open Chom Synthesis tracks
  • lines changed 3, context: html, text, full: html, text
    Added uncBsuProt
  • lines changed 3, context: html, text, full: html, text
    ch-ch-ch-chia pet
  • lines changed 3, context: html, text, full: html, text
    separated include line for UW Histone into its own section, added release tags to inlcude (staging on beta), removed alpha lines from wgEncodeUwHistone.ra in favor of release tags on include lines
  • lines changed 12, context: html, text, full: html, text
    added new composite HaibGenotype (CNV), created a new trackDb, added line to trackDb.wgEncode, added a new metaDb/alpha file, added a line to the makefile, added the bedLogR type to tagTypes.tab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 1, context: html, text, full: html, text
    adding space between number and units; changing the case of the S in ChIP-seq
  • lines changed 10, context: html, text, full: html, text
    alphabetizing the references list
  • lines changed 24, context: html, text, full: html, text
    changed this to release 1 for hg19, added link to hg18 hgTrackUi for info on hg18 releases, removed info about hg18 releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 296, context: html, text, full: html, text
    Katrina has standards for longLabels
  • lines changed 1, context: html, text, full: html, text
    Fixing the longLabel of the composite per the label approved by Kate
  • lines changed 289, context: html, text, full: html, text
    Added '-' in longLabel for clarity
  • lines changed 289, context: html, text, full: html, text
    Forgot to hit save before last check-in. Forgot the 's' in Modification
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 30, context: html, text, full: html, text
    separating Caltech into 2 releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 190, context: html, text, full: html, text
    separating Caltech into 2 releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 1586, context: html, text, full: html, text
    breaking up the Caltech track into two releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 1032, context: html, text, full: html, text
    breaking up the Caltech track into two releases
  • lines changed 1, context: html, text, full: html, text
    separating Caltech into 2 releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 156, context: html, text, full: html, text
    updated the track description with the new one from carrie
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html
  • lines changed 158, context: html, text, full: html, text
    Update to wgEncodeCshlLongRnaSeq.new.html
  • lines changed 158, context: html, text, full: html, text
    there is not a second release, there does not need to be a .new file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 118, context: html, text, full: html, text
    added two more experiments and fixed the on/off defaults
  • lines changed 1384, context: html, text, full: html, text
    edited short and long labels of new experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 2125, context: html, text, full: html, text
    added 56 new experiments for CSHLShort Release 2
  • lines changed 129, context: html, text, full: html, text
    fix up the braney docId mistake
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 142, context: html, text, full: html, text
    ch-ch-ch-chia pet
  • lines changed 16, context: html, text, full: html, text
    add interaction type
  • lines changed 29, context: html, text, full: html, text
    clean up GisGhiaPet... try to get score filtering to work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 60, context: html, text, full: html, text
    Added 2 new experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 885, context: html, text, full: html, text
    added new composite HaibGenotype (CNV), created a new trackDb, added line to trackDb.wgEncode, added a new metaDb/alpha file, added a line to the makefile, added the bedLogR type to tagTypes.tab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 17, context: html, text, full: html, text
    added 2 more experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 129, context: html, text, full: html, text
    added the composite HAIB RNA-seq. The metaData is loaded, but the tracks are not
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 49, context: html, text, full: html, text
    added the composite HAIB RNA-seq. The metaData is loaded, but the tracks are not
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 367, context: html, text, full: html, text
    Added 10 Chip-seq submissions for the Jan 2011 freeze.
  • lines changed 4, context: html, text, full: html, text
    fix up the braney docId mistake
  • lines changed 73, context: html, text, full: html, text
    Added 4 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
  • lines changed 29, context: html, text, full: html, text
    fixed typo, removed some <br> in favor of <p> & </p> tags, formatted the references
  • lines changed 6, context: html, text, full: html, text
    Revised the text on histone families, by suggestion of Katrina
  • lines changed 1, context: html, text, full: html, text
    Added mention of histone H5 to the track description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 187, context: html, text, full: html, text
    Updated a l;ot of long and short labels to the preferred style
  • lines changed 164, context: html, text, full: html, text
    New submissions for Chip and Faire. More label fixing.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 271, context: html, text, full: html, text
    Updated a l;ot of long and short labels to the preferred style
  • lines changed 8, context: html, text, full: html, text
    New submissions for Chip and Faire. More label fixing.
  • lines changed 1, context: html, text, full: html, text
    Changed the ordering in the ENCODE DNase/FAIRE supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 121, context: html, text, full: html, text
    Updated a l;ot of long and short labels to the preferred style
  • lines changed 128, context: html, text, full: html, text
    New submissions for Chip and Faire. More label fixing.
  • lines changed 6, context: html, text, full: html, text
    Fixed accidental docId based names. Mdb was okay
  • lines changed 1, context: html, text, full: html, text
    Changed the ordering in the ENCODE DNase/FAIRE supertrack
  • lines changed 28, context: html, text, full: html, text
    Addition of last submission for freeze
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 113, context: html, text, full: html, text
    Initial checkin of Open Chom Synthesis tracks
  • lines changed 2, context: html, text, full: html, text
    Changed the ordering in the ENCODE DNase/FAIRE supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 1943, context: html, text, full: html, text
    Separating Riken into a release 2 and adding 10 more experiments
  • lines changed 249, context: html, text, full: html, text
    Added signals to the second release, this caused many issues as they used to be called clusters
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 184, context: html, text, full: html, text
    Separating Riken into a release 2 and adding 10 more experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 8, context: html, text, full: html, text
    staging Suny Tiling, redmine issue #38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 521, context: html, text, full: html, text
    Added 29 submissions for the Jan 2011 Freeze. Also, removed commented lines out of trackDb and reorder treatment and antibodies in alphabetical order.
  • lines changed 1, context: html, text, full: html, text
    Reordered tratments alphabetically.Missed in last commit.
  • lines changed 4, context: html, text, full: html, text
    fix up the braney docId mistake
  • lines changed 101, context: html, text, full: html, text
    Added 5 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 115, context: html, text, full: html, text
    Added two new antibodies and one antibody validation document. I'd tried before, but messed up with git stash
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 55, context: html, text, full: html, text
    Added two new antibodies and one antibody validation document. I'd tried before, but messed up with git stash
  • lines changed 4, context: html, text, full: html, text
    Added uncBsuProt
  • lines changed 2, context: html, text, full: html, text
    Cleaned up the composite name
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the ordering in the ENCODE DNase/FAIRE supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the ordering in the ENCODE DNase/FAIRE supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 423, context: html, text, full: html, text
    separated include line for UW Histone into its own section, added release tags to inlcude (staging on beta), removed alpha lines from wgEncodeUwHistone.ra in favor of release tags on include lines
  • lines changed 424, context: html, text, full: html, text
    Removed errant space in shortlabl for 1 subtrack. ast by ChIP-seq to subtrack long labels to following track settings style guide.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    Stuff for Hapmap tracks lift to hg19 (SNPs and LD Phased)
  • lines changed 20, context: html, text, full: html, text
    pushing agilent track from alpha to beta for hg19, mm9 and rn4
• src/hg/makeDb/trackDb/mouse/agilentCghAlpha.html
  • lines changed 1, context: html, text, full: html, text
    fixing the count(*) in the table so matches for agilent1x1m subtrack
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 403, context: html, text, full: html, text
    Added 5 submissions with Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 537, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added LICR Histone track.
  • lines changed 3, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 151, context: html, text, full: html, text
    Added 5 submissions with Peaks and Signals which previously only had raw data files.
  • lines changed 2, context: html, text, full: html, text
    Changed Long and Short labels to comply with track configuration standards.
  • lines changed 1, context: html, text, full: html, text
    Added noInherit on to both tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 173, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
  • lines changed 2, context: html, text, full: html, text
    Changed Long and Short labels to comply with track configuration standards.
  • lines changed 1, context: html, text, full: html, text
    Added noInherit on to both tracks.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    pushing agilent track from alpha to beta for hg19, mm9 and rn4
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    pushing agilent track from alpha to beta for hg19, mm9 and rn4
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 258, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): First cut of description. Still needs to describe the new columns, and when implemented, the new coloring/filtering controls on the new columns.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    added bigWig to maxWindowsToDraw
  • lines changed 2, context: html, text, full: html, text
    clean up GisGhiaPet... try to get score filtering to work
  • lines changed 4, context: html, text, full: html, text
    added new composite HaibGenotype (CNV), created a new trackDb, added line to trackDb.wgEncode, added a new metaDb/alpha file, added a line to the makefile, added the bedLogR type to tagTypes.tab
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
  • lines changed 28, context: html, text, full: html, text
    Edited this text and replaced incorrect zv8 information (cut/paste error from previous version?) with new zv9 info.
  • lines changed 1, context: html, text, full: html, text
    adding in missing comma. Is now consistent with index page
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 186, context: html, text, full: html, text
    composite containers for the chains and nets
• src/hg/oneShot/doOmimGeneSymbols/doOmimGeneSymbols.c
  • lines changed 81, context: html, text, full: html, text
    Created doOmimGeneSymbols.c for OMIM releated subtracks build pipeline.
• src/hg/oneShot/doOmimGeneSymbols/makefile
  • lines changed 38, context: html, text, full: html, text
    Created makefile for OMIM releated subtracks build pipeline.
• src/hg/txGene/makefile
  • lines changed 1, context: html, text, full: html, text
    Created a subdirectory of utility scripts used for testing UCSC Genes. This might not be the ideal place for this subdirectory, or even the right subdirectory organization, but I wanted to just get these scripts under revision control. They can always be moved again later
• src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh
  • lines changed 20, context: html, text, full: html, text
    Created a subdirectory of utility scripts used for testing UCSC Genes. This might not be the ideal place for this subdirectory, or even the right subdirectory organization, but I wanted to just get these scripts under revision control. They can always be moved again later
  • lines changed 21, context: html, text, full: html, text
    Added some usage information
• src/hg/txGene/txGeneValidation/compareRandomSample.py
  • lines changed 40, context: html, text, full: html, text
    Created a subdirectory of utility scripts used for testing UCSC Genes. This might not be the ideal place for this subdirectory, or even the right subdirectory organization, but I wanted to just get these scripts under revision control. They can always be moved again later
• src/hg/txGene/txGeneValidation/makefile
  • lines changed 7, context: html, text, full: html, text
    Created a subdirectory of utility scripts used for testing UCSC Genes. This might not be the ideal place for this subdirectory, or even the right subdirectory organization, but I wanted to just get these scripts under revision control. They can always be moved again later
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 1, context: html, text, full: html, text
    Adding blank line after initial comment.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • lines changed 34, context: html, text, full: html, text
    trying this without the fork business
  • lines changed 154, context: html, text, full: html, text
    this runs 2X faster without the fork business
  • lines changed 2, context: html, text, full: html, text
    remove bogus hConnectCentral and Disconnect
  • lines changed 210, context: html, text, full: html, text
    going back to the forking, but forking only 10 times by default instead of 16000, should still reduce peak ram usage from 3GB to just 300MB and still run fast
  • lines changed 4, context: html, text, full: html, text
    timeout up to 40 minutes for one fork
• src/utils/bedRemoveOverlap/bedRemoveOverlap.c
  • lines changed 151, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/empty.expected
  • lines changed 0, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/makefile
  • lines changed 33, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
  • lines changed 6, context: html, text, full: html, text
    Cleaning up after test.
• src/utils/bedRemoveOverlap/one.expected
  • lines changed 1, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/test4.expected
  • lines changed 4, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/threeLast.expected
  • lines changed 1, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/twoFirst.expected
  • lines changed 1, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/twoSecond.expected
  • lines changed 1, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/bedRemoveOverlap/unsorted.expected
  • lines changed 0, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new bedRemoveOverlap utility.
• src/utils/qa/countPerChrom.csh
  • lines changed 46, context: html, text, full: html, text
    reworked so histogram scale is the same on both sides if comparing two datasets. added statement about max value and value of each x, so scale makes more sense
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v246 final build

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• files changed: 302