All File Changes

v253_preview to v253_preview2 (2011-06-14 to 2011-06-21) v253

• src/hg/checkCoverageGaps/checkCoverageGaps.c
  • lines changed 216, context: html, text, full: html, text
    First cut of utility to check for coverage gaps in a track. Doesn't work for bigBeds yet.
  • lines changed 25, context: html, text, full: html, text
    Adding bigBed support
  • lines changed 45, context: html, text, full: html, text
    Commenting and making it only open the bbiFile once, rather than once per chrom.
• src/hg/checkCoverageGaps/makefile
  • lines changed 18, context: html, text, full: html, text
    First cut of utility to check for coverage gaps in a track. Doesn't work for bigBeds yet.
• src/hg/encode/DAFs/2.0/caltechMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAF's to have replicates required for peaks and signals.
• src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAF's to have replicates required for peaks and signals.
• src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf
  • lines changed 60, context: html, text, full: html, text
    First pass at DAF for UW RNA-seq data.
• src/hg/hgTables/bam.c
  • lines changed 1, context: html, text, full: html, text
    Bug #4302 (link in table schema for BAM files gives a 404):Fixed broken link to SAM spec, and removed dead code (that had the correct link but is no longer exercised).
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    Bug #4302 (link in table schema for BAM files gives a 404):Fixed broken link to SAM spec, and removed dead code (that had the correct link but is no longer exercised).
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    Commented out the 'Others' option for omimLocatioocation for the time being.
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Add NCBI link to bosTau6's blue top bar
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    Fixed redmine 4151: hgTracks should generated HREF=../cgi-bin for hgGene
  • lines changed 1, context: html, text, full: html, text
    Fixed redmine 4151: hgTracks should generated HREF=../cgi-bin for hgGene
• src/hg/hgTracks/snakeTrack.c
  • lines changed 435, context: html, text, full: html, text
    packed snakes work pretty well now. Probably we should lose the full mode. Probably it doesn't work with blocks on multiple chroms, but it's working fairly well with the MHC reconstructions which is the short-term goal
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    adding Duke Affy Exon, redmine #60
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    Andy made it so that colorByStrand in custom tracks works for BED6-BED8. Updating documentation to reflect that: http://redmine.soe.ucsc.edu/issues/1377
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 51, context: html, text, full: html, text
    tidying up announcements on home page and archive page
  • lines changed 56, context: html, text, full: html, text
    added news about OMIM release
  • lines changed 4, context: html, text, full: html, text
    added/fixed link to omim's downloads
• src/hg/htdocs/images/leftBlue.png
  • lines changed 0, context: html, text, full: html, text
    Added left and right arrow triangle thingies for Kate.
• src/hg/htdocs/images/rightBlue.png
  • lines changed 0, context: html, text, full: html, text
    Added left and right arrow triangle thingies for Kate.
• src/hg/htdocs/indexNews.html
  • lines changed 32, context: html, text, full: html, text
    tidying up announcements on home page and archive page
  • lines changed 53, context: html, text, full: html, text
    added news about OMIM release
  • lines changed 4, context: html, text, full: html, text
    added/fixed link to omim's downloads
  • lines changed 34, context: html, text, full: html, text
    too many announcements on home page
• src/hg/jaxMgi/parseAllele.pl
  • lines changed 92, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/jaxMgi/parsePhenotype.pl
  • lines changed 61, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/jaxMgi/parsePhenotypicAllele.pl
  • lines changed 100, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/jaxMgi/parseRepTranscript.pl
  • lines changed 68, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    Fixed Brooke's find of track set hide reappearing on refresh as described in redmine 4119
• src/hg/lib/customFactory.c
  • lines changed 16, context: html, text, full: html, text
    plugging potential security problem by not allowing bigDataUrl to contain local file references - only http, https, or ftp are allowed. Give user informative error message and abort
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    Uncommenting hTrackINfo
• src/hg/lib/jksql.c
  • lines changed 3, context: html, text, full: html, text
    flush stderr when priting monitor messages
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 6, context: html, text, full: html, text
    Create pushQ entries for bosTau6.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV7.release1.notes
  • lines changed 58, context: html, text, full: html, text
    adding a notes file for GencodeV7
• src/hg/makeDb/doc/mm9.txt
  • lines changed 217, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 20, context: html, text, full: html, text
    added panTro3 N-SCAN predictions
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Updated percetages of OMIM related IDs.
  • lines changed 4, context: html, text, full: html, text
    Added ceuBcellRNASeqId.
  • lines changed 3, context: html, text, full: html, text
    Added ceuBcellRNASeqBW to ignore list.
  • lines changed 2, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19
• src/hg/makeDb/trackDb/chimp/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for KRIBB
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    added panTro3 N-SCAN predictions
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 70, context: html, text, full: html, text
    Polished detail description, gap, gold html files
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
  • lines changed 47, context: html, text, full: html, text
    Polished detail description, gap, gold html files
• src/hg/makeDb/trackDb/cow/bosTau6/gold.html
  • lines changed 3, context: html, text, full: html, text
    Polished detail description, gap, gold html files
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 31, context: html, text, full: html, text
    Remove redundant all_mrna and all_est tracks entries
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 39, context: html, text, full: html, text
    Updated the coloring shcema for mouse cell/tissues based on Redmine #3990. Also updated tissue of Muscle and Myocyte to be Muscles instead of blood. Limb and Placenta coloring needs to be worked on, will do more research, but added temporary coloring.
  • lines changed 2, context: html, text, full: html, text
    Changed coloring for Limb to Skeletal, makes the most sense at the moment. Also updated Placenta to be circulatory, as this is one of the main functions.
  • lines changed 616, context: html, text, full: html, text
    Housekeeping changes: (1) finished converting the tags to uppercase, so that no one mistakenly enters mixed-case tags in code review (without an excuse) again, (2) added tags to th stanzas that don't have tags, to give the validator a nice, general schema to work with, and (3) removed a handful of stanzas that have been commented out for eons, as well as a couple recent ones which I know to not be needed anymore
  • lines changed 107, context: html, text, full: html, text
    Addressing code review feedback from Jim. A lot of this involves dealing with single-token lines in the ra stanzas (i.e. a label but no contents), which is apparently undefined in the formal ra specification
  • lines changed 24, context: html, text, full: html, text
    Addressing code review feedback from Katrina
  • lines changed 113, context: html, text, full: html, text
    (1) Addressing Jim's code review comments, (2) housekeeping: making all tags uppercase and making sure all stanzas have tags, plus removing some cruft that's not needed anymore
  • lines changed 4, context: html, text, full: html, text
    changed DMSO tags to be all upper case
  • lines changed 1, context: html, text, full: html, text
    corrected some other capitalization errors in cv.
  • lines changed 42, context: html, text, full: html, text
    (1) bug fix: one stanza had lost its type and description, causing anything that displays cv material to blow up (2) I had somehow stomped on Venkat's new colors, and reinstated them to the best of my ability
  • lines changed 5, context: html, text, full: html, text
    Fixed accidental mouse color reversions to match correct designation as Redmine 3990 and match commit 06dfd5c15b45b6253fa07b9599e799ca6b56ca56.
  • lines changed 11, context: html, text, full: html, text
    New lineage definitions
  • lines changed 6, context: html, text, full: html, text
    Added three new protocols for the Stam lab
  • lines changed 1, context: html, text, full: html, text
    Fixing a missing step in adding a new protocol document for the Stam lab
  • lines changed 2, context: html, text, full: html, text
    Added a couple new lineages
  • lines changed 11, context: html, text, full: html, text
    Still cleaning up from last week's code review...
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeq.html
  • lines changed 84, context: html, text, full: html, text
    Fixed html formatting: closed tags, indented blocks, made tags lowercase, added p tags, hard wrapped lines to 100 characters, etc.
  • lines changed 41, context: html, text, full: html, text
    Fixed grammar, citation formats, etc. Added relavant links. Cleaned up line wrapping.
  • lines changed 7, context: html, text, full: html, text
    Added a new publication to hg18/ceuBcellRNASeq.html.
  • lines changed 13, context: html, text, full: html, text
    added newly-published paper and cleaned up other citations
• src/hg/makeDb/trackDb/human/hg18/evoCpg.html
  • lines changed 3, context: html, text, full: html, text
    Fixed typo and added link for article
  • lines changed 1, context: html, text, full: html, text
    Added color shade description for evoCpg track.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 47, context: html, text, full: html, text
    Removed duplcate objects on request from lab: wgEncodeHudsonalphaChipSeqRawSignalRep2Pfsk1Control and wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Control.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata on beta, redmine 2882
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBroadHmm.ra
  • lines changed 168, context: html, text, full: html, text
    staging metadata on beta, redmine 2882
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 82, context: html, text, full: html, text
    Re-lable the lonngLabel of NumtS tracks for hg18, hg19 and mm9.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
  • lines changed 20, context: html, text, full: html, text
    edits to theh Broad HMM track descriptions, redmine #2882
  • lines changed 1, context: html, text, full: html, text
    adding missing comma, redmine 2882
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 9, context: html, text, full: html, text
    staging on beta, redmine 2882
  • lines changed 2, context: html, text, full: html, text
    Removed score from hgc and addied (Tier 1) to cell line titles.
  • lines changed 10, context: html, text, full: html, text
    Also force sort order to be by tier then cell line.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 7, context: html, text, full: html, text
    Removed duplcate objects on request from lab: wgEncodeHudsonalphaChipSeqRawSignalRep2Pfsk1Control and wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Control.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 529, context: html, text, full: html, text
    loaded submissions 4308 - 4312 (5 total)
  • lines changed 153, context: html, text, full: html, text
    removed entries that were v2'ed
  • lines changed 6, context: html, text, full: html, text
    changed the date restricted to match the old v1 entries of things that were v2'ed
  • lines changed 25, context: html, text, full: html, text
    added dcc and expid to the newly added submissions
  • lines changed 107, context: html, text, full: html, text
    removed metadata entries for v1 objects that appear in metadb only
  • lines changed 1, context: html, text, full: html, text
    forgot to regenerate magic number
  • lines changed 2, context: html, text, full: html, text
    changed the date unrestricted for the weird rep3 entries
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
  • lines changed 1004, context: html, text, full: html, text
    regenerated magic numbers for sydh tfbs, sydh histone, and caltech rna. for some reason caltech rnaseq didn't get added for the name change redmine #3608, so i'm adding it now.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2475, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 57, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
  • lines changed 543, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 193, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 225, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 175, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 147, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 227, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 72, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
  • lines changed 371, context: html, text, full: html, text
    found some composites i missed
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 24, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 45, context: html, text, full: html, text
    added in subId 4332 to riken cage
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 49, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 17, context: html, text, full: html, text
    found some composites i missed
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 1, context: html, text, full: html, text
    regenerated magic numbers for sydh tfbs, sydh histone, and caltech rna. for some reason caltech rnaseq didn't get added for the name change redmine #3608, so i'm adding it now.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 125, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 171, context: html, text, full: html, text
    Initial meta-data corrections to make sure experiments are correctly parsed for hg19.
  • lines changed 69, context: html, text, full: html, text
    Removed duplicate meta-data and raw-data files for K562 GTF2b experiment. Also correct type in load of GM12878 WHIP as GM112878 XRCC4. Delete older copy of GM12878 WHIP and Replaced with new file and update meta-data.
  • lines changed 22, context: html, text, full: html, text
    Removed old rawData file: wgEncodeSydhTfbsK562InputRawData that was moved from hg18 but has substitued data on hg19.
  • lines changed 1641, context: html, text, full: html, text
    Updated lab meta-data so that experimetns would group together and would have same Ids as hg18.
  • lines changed 97, context: html, text, full: html, text
    Merged in changes that added 120 Peaks provided by awg.
  • lines changed 545, context: html, text, full: html, text
    Accidently committed meta-data file over trackDb file: 58d9a475183299f90ca6eb4ad34d31aa3cf01b52. Now did:Updated lab information for experiments such that they will group with the correct experiment number.
  • lines changed 63, context: html, text, full: html, text
    Added back metadata for submission 4119.
  • lines changed 64, context: html, text, full: html, text
    Added 3 missing Signals for track. Resolves redmine #3996.
  • lines changed 72, context: html, text, full: html, text
    Addedmissing bams for 2 experiemnts. Resolves issue in redmine #78. Also loaded bam's that were once concatenated submission 1625 and 1623 using samtools merge instead of cat. Resolves issue in redmine #3216.
  • lines changed 1, context: html, text, full: html, text
    regenerated magic numbers for sydh tfbs, sydh histone, and caltech rna. for some reason caltech rnaseq didn't get added for the name change redmine #3608, so i'm adding it now.
  • lines changed 24, context: html, text, full: html, text
    Added last missing bam. Resolves Redmine #78
  • lines changed 63, context: html, text, full: html, text
    added missing metadata from sub 4119
  • lines changed 4, context: html, text, full: html, text
    merged
  • lines changed 2, context: html, text, full: html, text
    reverted
  • lines changed 1157, context: html, text, full: html, text
    added expid's and dcc accession to sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 17, context: html, text, full: html, text
    added in expId's and dccAccession's to tracks that were missing them (lots)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 7, context: html, text, full: html, text
    Checking in a fresh version of the uncBsuProt metadata
  • lines changed 17, context: html, text, full: html, text
    Added DCC accessions for a few new subtracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 6, context: html, text, full: html, text
    Added the composite definition
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata on beta, redmine 2882
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHmm.ra
  • lines changed 186, context: html, text, full: html, text
    staging metadata on beta, redmine 2882
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing to release Duke Affy Exon Array, redmine#60
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeDukeAffyExon.ra
  • lines changed 2369, context: html, text, full: html, text
    preparing to release Duke Affy Exon Array, redmine#60
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 76, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19 and mm9
• src/hg/makeDb/trackDb/human/hg19/pgSnpHgwdev.html
  • lines changed 331, context: html, text, full: html, text
    Added new personal genomes to pgSnpHgwdev track, not all will be lifted anymore
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 75, context: html, text, full: html, text
    Re-lable the lonngLabel of NumtS tracks for hg18, hg19 and mm9.
  • lines changed 1, context: html, text, full: html, text
    don't force next item buttons to be always on
  • lines changed 120, context: html, text, full: html, text
    Added new personal genomes to pgSnpHgwdev track, not all will be lifted anymore
  • lines changed 3, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 100, context: html, text, full: html, text
    loaded submissions 4308 - 4312 (5 total)
  • lines changed 52, context: html, text, full: html, text
    removed entries that were v2'ed
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 21, context: html, text, full: html, text
    edits to theh Broad HMM track descriptions, redmine #2882
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 9, context: html, text, full: html, text
    staging on beta, redmine 2882
  • lines changed 20, context: html, text, full: html, text
    removing mention of lift in long/short Labels. Adding origAssembly line to composite stanza
  • lines changed 2, context: html, text, full: html, text
    Removed score from hgc and addied (Tier 1) to cell line titles.
  • lines changed 10, context: html, text, full: html, text
    Also force sort order to be by tier then cell line.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 2, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 121, context: html, text, full: html, text
    changed the long labels for the junction submissions and some other ones
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 54, context: html, text, full: html, text
    removing the origAssembly hg18 so that it doesn't look like it is via liftover
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 8, context: html, text, full: html, text
    fixed typos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 5, context: html, text, full: html, text
    changed tags to be all caps in the hib tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 24, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
  • lines changed 67, context: html, text, full: html, text
    changed tags to be all caps in the hib tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 81, context: html, text, full: html, text
    changed tags to be all caps in the hib tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 8, context: html, text, full: html, text
    changed a whole bunch of object names according to a list jeff gave me, Redmine #3608
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 16, context: html, text, full: html, text
    added in subId 4332 to riken cage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
  • lines changed 48, context: html, text, full: html, text
    cleaned up suny switchgear html according to redmine #169
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 10, context: html, text, full: html, text
    Removed duplicate meta-data and raw-data files for K562 GTF2b experiment. Also correct type in load of GM12878 WHIP as GM112878 XRCC4. Delete older copy of GM12878 WHIP and Replaced with new file and update meta-data.
  • lines changed 287, context: html, text, full: html, text
    Merged in changes that added 120 Peaks provided by awg.
  • lines changed 38937, context: html, text, full: html, text
    Updated lab information for experiments such that they will group with the correct experiment number.
  • lines changed 38937, context: html, text, full: html, text
    Accidently committed meta-data file over trackDb file: 58d9a475183299f90ca6eb4ad34d31aa3cf01b52. Now did:Updated lab information for experiments such that they will group with the correct experiment number.
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    Added 3 missing Signals for track. Resolves redmine #3996.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 35, context: html, text, full: html, text
    Updated with a new version provided by Jainab. The differences seem to pertain to how the data is now filtered by default, with the displayed data now having an estimated FDR of 5%, not 10%.
  • lines changed 1, context: html, text, full: html, text
    Minor correction on how the EValue is computed
• src/hg/makeDb/trackDb/human/omimDescriptionText.html
  • lines changed 11, context: html, text, full: html, text
    added comment about downloads
  • lines changed 5, context: html, text, full: html, text
    added comment about downloads
  • lines changed 1, context: html, text, full: html, text
    Added a period.
  • lines changed 25, context: html, text, full: html, text
    added a description of the three tracks to go at the top of all three
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 2, context: html, text, full: html, text
    Added a line about the hgTrackUi controls.
• src/hg/makeDb/trackDb/human/omimLocation.html
  • lines changed 5, context: html, text, full: html, text
    Removed description of Light Gray entries, as Fan removed these from the table at the request of OMIM. Edited methods section to reflect change. Fan approved in RM #2153, note-168.
  • lines changed 2, context: html, text, full: html, text
    Added a line about the hgTrackUi controls.
• src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
  • lines changed 1234, context: html, text, full: html, text
    Added new personal genomes to pgSnpHgwdev track, not all will be lifted anymore
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Making OMIM tables unavailable in table browser, at least for now. (Per Redmine #2153.)
  • lines changed 94, context: html, text, full: html, text
    Re-lable the lonngLabel of NumtS tracks for hg18, hg19 and mm9.
  • lines changed 252, context: html, text, full: html, text
    Added new personal genomes to pgSnpHgwdev track, not all will be lifted anymore
  • lines changed 18, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19
  • lines changed 1, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19 and mm9
• src/hg/makeDb/trackDb/mouse/jaxPhenotype.html
  • lines changed 96, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): got new data from BobSinclair at MGI. There are a couple new phenotypes, that apparently have subsumed a few of the old phenotypes; I added links to MGI's Mammalian Phenotype Browser pages from our details page's table of phenotypes. The files from MGI include both old and new phenotypes. Finally moved the 5+ year old perl scripts into the source tree instead of inlining them (or not) in mm9.txt.
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
  • lines changed 93, context: html, text, full: html, text
    Corrected grammar so that it didn't read as we (the lab). Corrected some odd formating on the image. Corrected citation formats. And maybe a couple minor other html tweaks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 147, context: html, text, full: html, text
    Added submission 3057.
  • lines changed 41, context: html, text, full: html, text
    Updated meta-data and file and obj names with resbumitted bam's. Fixes Redmine Issue #2006.
  • lines changed 13, context: html, text, full: html, text
    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
  • lines changed 2, context: html, text, full: html, text
    Updated expVars for these tracks to include control, so that the correct inputs are experimentified.
  • lines changed 4, context: html, text, full: html, text
    Updated lab for bam files to match lab of other files for an experiment.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 10, context: html, text, full: html, text
    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 176, context: html, text, full: html, text
    Updated meta-data and file and obj names with resbumitted bam's. Fixes Redmine Issue #2006.
  • lines changed 26, context: html, text, full: html, text
    Removed meta-data for non-existant fastq and update file name for wgEncodeSydhTfbsMelInputStdAlnRep1 so that metaCheck would not complain.
  • lines changed 26, context: html, text, full: html, text
    Removed wgEncodeSydhTfbsMelInputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
  • lines changed 25, context: html, text, full: html, text
    Removed wgEncodeSydhTfbsCh12InputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
  • lines changed 59, context: html, text, full: html, text
    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
  • lines changed 7, context: html, text, full: html, text
    Added last fixed alignment wgEncodeSydhTfbsCh12InputIggrabAln, update object and file names.Fixes Redmine Issue #2006
  • lines changed 2, context: html, text, full: html, text
    Updated expVars for these tracks to include control, so that the correct inputs are experimentified.
  • lines changed 5, context: html, text, full: html, text
    Updated the correct meta-data for resubmitted Mel Max files. SubId 4157.
  • lines changed 5, context: html, text, full: html, text
    Revert "Updated the correct meta-data for resubmitted Mel Max files. SubId 4157." This reverts commit f3565a8b9028b97b8607b02f03173190255a5728.
  • lines changed 9, context: html, text, full: html, text
    Updated the correct meta-data for resubmitted Mel Max files (IgG-rab control instead of IgG-mus). SubId 4157.
  • lines changed 8, context: html, text, full: html, text
    Renamed 4 files for renaming DMSO Experiments that were missed earlier.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 2, context: html, text, full: html, text
    staging LICR Histone mm9 on beta, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrHistone.ra
  • lines changed 4968, context: html, text, full: html, text
    staging LICR Histone mm9 on beta, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 17, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19 and mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Removing forelimbH3k27ac track which I just put in to teach someone how to add tracks at CSHL meeting.
  • lines changed 5, context: html, text, full: html, text
    Re-lable the lonngLabel of NumtS tracks for hg18, hg19 and mm9.
  • lines changed 75, context: html, text, full: html, text
    Dealing with merge conflicts.
  • lines changed 23, context: html, text, full: html, text
    Finished NumtSeq track for mm9
  • lines changed 1, context: html, text, full: html, text
    Finished NumtSeq tracks for hg19 and mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging LICR Histone mm9 on beta, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 2, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
  • lines changed 6, context: html, text, full: html, text
    made description into more of a paragraph format for LICR Histone, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
  • lines changed 4, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
  • lines changed 4, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 21, context: html, text, full: html, text
    Added submission 3057.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 2, context: html, text, full: html, text
    Renamed 4 files for renaming DMSO Experiments that were missed earlier.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 17, context: html, text, full: html, text
    Updated the ordering of the references to be alphabtically by first author. Added periods after article name to match standard. Redmine 191, note 17.
• src/hg/makefile
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    Adding checkCoverageGaps to make
  • lines changed 2, context: html, text, full: html, text
    Adding checkCoverageGaps to make
• src/lib/bbiRead.c
  • lines changed 1, context: html, text, full: html, text
    fixed file handle leak in bbiFileCheckSigs()
• src/lib/common.c
  • lines changed 4, context: html, text, full: html, text
    a bit of extra information on the buffer overflow message to maybe help locate the message short of a stack dump at this point
• src/lib/https.c
  • lines changed 2, context: html, text, full: html, text
    The right way to set the port, the old way probably did not work for other than the default https port.
• src/utils/qa/weeklybld/buildEnv.csh
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    v253 preview2

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