File Changes for cricket

v258_base to v259_preview (2011-10-10 to 2011-10-25) v259

• python/programs/qaInit/qaInit
  • lines changed 8, context: html, text, full: html, text
    some corrections for situations when not all tracks have certain objects
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    Adding Chromatin Intereactions and UW 5C to the downloads for release
  • lines changed 1, context: html, text, full: html, text
    Spelling out Univeristy
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 12, context: html, text, full: html, text
    Adding new comments about the order of type of term
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 268, context: html, text, full: html, text
    Checking in md5sums
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 35, context: html, text, full: html, text
    Alphabetizing the makefiles
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 856, context: html, text, full: html, text
    Moving geoSample to geoSampleAccession, Caltech(Wold) to Caltech and a few view changes, also worked on the commented out fileSortOrder in case we ever want to use it
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
  • lines changed 541, context: html, text, full: html, text
    Updating objStatus for Chromatin map with expId and objStatus
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDnaseSeq.ra
  • lines changed 998, context: html, text, full: html, text
    Staging UW Dnase hg18 to beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 35, context: html, text, full: html, text
    Alphabetizing the makefiles
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 856, context: html, text, full: html, text
    Moving geoSample to geoSampleAccession, Caltech(Wold) to Caltech and a few view changes, also worked on the commented out fileSortOrder in case we ever want to use it
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
  • lines changed 541, context: html, text, full: html, text
    Updating objStatus for Chromatin map with expId and objStatus
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDnaseSeq.ra
  • lines changed 998, context: html, text, full: html, text
    Releaseing UW Dnase Release 5 hg18
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging UW Dnase hg18 to beta
  • lines changed 2, context: html, text, full: html, text
    Releaseing UW Dnase Release 5 hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 1256, context: html, text, full: html, text
    This is more out of date than the .ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Moving geoSample to geoSampleAccession, Caltech(Wold) to Caltech and a few view changes, also worked on the commented out fileSortOrder in case we ever want to use it
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • lines changed 24, context: html, text, full: html, text
    Releaseing UW Dnase Release 5 hg18
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
  • lines changed 3, context: html, text, full: html, text
    Changing a few spelling errors and the link to hgdownload-test
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Releaseing UW Dnase Release 5 hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 26, context: html, text, full: html, text
    I am trying to clean up these makefiles to be alphabetical so that they are consistent. I am also removing metaData that has been replaced on public (Gencode is now Gencode4)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 16, context: html, text, full: html, text
    Adding the explicit bam,bai
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 103, context: html, text, full: html, text
    A bunch of small changes on HaibMethyl450, in prgress
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Removing old files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 6, context: html, text, full: html, text
    Removing old files
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 43, context: html, text, full: html, text
    Alphabetizing the makefiles
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeDukeAffyExon.ra
  • lines changed 156, context: html, text, full: html, text
    Staging Duke Affy Exon release 2 for public
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
  • lines changed 99, context: html, text, full: html, text
    I am trying to clean up these makefiles to be alphabetical so that they are consistent. I am also removing metaData that has been replaced on public (Gencode is now Gencode4)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 94, context: html, text, full: html, text
    Staging for public SYDH Histone mini fix release
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 654, context: html, text, full: html, text
    Staging UW Dnase for public
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging UW 5C for public
  • lines changed 43, context: html, text, full: html, text
    I am trying to clean up these makefiles to be alphabetical so that they are consistent. I am also removing metaData that has been replaced on public (Gencode is now Gencode4)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeDukeAffyExon.ra
  • lines changed 156, context: html, text, full: html, text
    Staging Duke Affy Exon release 2 for public
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencode.ra
  • lines changed 99, context: html, text, full: html, text
    I am trying to clean up these makefiles to be alphabetical so that they are consistent. I am also removing metaData that has been replaced on public (Gencode is now Gencode4)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 94, context: html, text, full: html, text
    Staging for public SYDH Histone mini fix release
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUw5C.ra
  • lines changed 766, context: html, text, full: html, text
    Staging UW 5C for public
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 4672, context: html, text, full: html, text
    Staging UW Dnase for public
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging UW 5C for public
  • lines changed 2, context: html, text, full: html, text
    Staging for public SYDH Histone mini fix release
  • lines changed 2, context: html, text, full: html, text
    Staging Duke Affy Exon release 2 for public
  • lines changed 4, context: html, text, full: html, text
    Changing the release tags to be file wide and not stanza wide
  • lines changed 2, context: html, text, full: html, text
    Staging UW Dnase for public
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 4, context: html, text, full: html, text
    Staging Duke Affy Exon release 2 for public
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 10, context: html, text, full: html, text
    Staging Duke Affy Exon release 2 for public
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 70, context: html, text, full: html, text
    A bunch of small changes on HaibMethyl450, in prgress
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.new.ra
  • lines changed 343, context: html, text, full: html, text
    This is the final file for the release tag change for wgEncodeReg
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 35, context: html, text, full: html, text
    Changing the release tags to be file wide and not stanza wide
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 3, context: html, text, full: html, text
    Staging for public SYDH Histone mini fix release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 8, context: html, text, full: html, text
    Staging for public SYDH Histone mini fix release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 4, context: html, text, full: html, text
    Small wording changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 1, context: html, text, full: html, text
    Changing long label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 32, context: html, text, full: html, text
    Staging UW Dnase for public
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 916, context: html, text, full: html, text
    Staging UW Dnase for public
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 10, context: html, text, full: html, text
    Alphabetizing the makefiles
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 5, context: html, text, full: html, text
    Alphabetizing the makefiles
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 4, context: html, text, full: html, text
    Alphabetizing the makefiles