mikep: changes by file

review to branch (2009-03-03 to 2009-03-10) v202

• src/hg/encode/DAFs/HelicosRnaSeq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Transfrags not required at this stage
• src/hg/encode/DAFs/WoldRnaSeq.daf
  • 1.5 lines changed: 12, context: html, text, full: html, text
    cant put pipeline data in daf as it doesnt have variables associated
  • 1.4 lines changed: 12, context: html, text, full: html, text
    adding rawdata files for Wold pipeline input data
  • 1.3 lines changed: 38, context: html, text, full: html, text
    updated DAF to handle more raw data files
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.57 lines changed: 3, context: html, text, full: html, text
    dont add name indexes onto this highthroughput data
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.165 lines changed: 1, context: html, text, full: html, text
    CS fasta can have G sequences evidnetly
  • 1.164 lines changed: 4, context: html, text, full: html, text
    open tars
  • 1.163 lines changed: 6, context: html, text, full: html, text
    diff header coming from GIS
  • 1.162 lines changed: 3, context: html, text, full: html, text
    maybe there are more rawdatas in future...
  • 1.161 lines changed: 6, context: html, text, full: html, text
    readType validator for Wold/Caltech
  • 1.160 lines changed: 2, context: html, text, full: html, text
    get rid of @_ deprecated warning
  • 1.159 lines changed: 20, context: html, text, full: html, text
    3 different flavors of rpkm; just check the cols are there
  • 1.158 lines changed: 6, context: html, text, full: html, text
    validator for frag size for GIS gDNA PET
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.84 lines changed: 1, context: html, text, full: html, text
    shorter codes
  • 1.82 lines changed: 1, context: html, text, full: html, text
    fixed typo
  • 1.81 lines changed: 9, context: html, text, full: html, text
    new variable readType for Caltech
  • 1.80 lines changed: 2, context: html, text, full: html, text
    removed some gnarly chars for javascript
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.19 lines changed: 10, context: html, text, full: html, text
    put the url around the term id
• src/hg/inc/versionInfo.h
  • 1.142 lines changed: 1, context: html, text, full: html, text
    "New version number v202"
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.200 lines changed: 89, context: html, text, full: html, text
    removing CSHL stuff while it is reprocessed
  • 1.199 lines changed: 183, context: html, text, full: html, text
    last tracks for RIKEN
  • 1.198 lines changed: 398, context: html, text, full: html, text
    added original Caltech data
  • 1.194 lines changed: 375, context: html, text, full: html, text
    adding second set of data, new cv.ra type
  • 1.193 lines changed: 24, context: html, text, full: html, text
    shortend name for table name
  • 1.192 lines changed: 1, context: html, text, full: html, text
    shorter codes
  • 1.191 lines changed: 8, context: html, text, full: html, text
    fixing up cell types by removing (+) chars
  • 1.190 lines changed: 188, context: html, text, full: html, text
    Reformatting Caltech tracks and description
  • 1.177 lines changed: 3, context: html, text, full: html, text
    friendlier labels
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    fixing tpyo
  • 1.8 lines changed: 63, context: html, text, full: html, text
    wrapping at 80 chars
  • 1.7 lines changed: 21, context: html, text, full: html, text
    adding data release policy, cell culture specs, and changing bold to italics
  • 1.6 lines changed: 27, context: html, text, full: html, text
    final adjustments to text
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added contact email
  • 1.4 lines changed: 5, context: html, text, full: html, text
    forgot A targets
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.8 lines changed: 4, context: html, text, full: html, text
    fixing view names
  • 1.7 lines changed: 3, context: html, text, full: html, text
    added link to downloads
  • 1.6 lines changed: 22, context: html, text, full: html, text
    added text for download file method
  • 1.5 lines changed: 88, context: html, text, full: html, text
    wrapping at 80 chars
  • 1.4 lines changed: 7, context: html, text, full: html, text
    adding links to publication (not in PubMed yet tho) and new cv.ra entry for reads
  • 1.3 lines changed: 29, context: html, text, full: html, text
    Reformatting Caltech tracks and description
  • 1.2 lines changed: 11, context: html, text, full: html, text
    adding boilerplate
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.3 lines changed: 23, context: html, text, full: html, text
    wrapping at 80 chars
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • 1.2 lines changed: 23, context: html, text, full: html, text
    wrapping at 80 chars
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.4 lines changed: 24, context: html, text, full: html, text
    wrapping at 80 chars
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.3 lines changed: 10, context: html, text, full: html, text
    adding standard text like Yale
  • 1.2 lines changed: 68, context: html, text, full: html, text
    last tracks for RIKEN
  • 1.1 lines changed: 134, context: html, text, full: html, text
    first draft of RIKEN doco
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
  • 1.9 lines changed: 20, context: html, text, full: html, text
    wrapping at 80 chars
  • 1.8 lines changed: 16, context: html, text, full: html, text
    adding data release policy, cell culture specs, and changing bold to italics
  • 1.7 lines changed: 2, context: html, text, full: html, text
    explain why a single view
  • 1.6 lines changed: 134, context: html, text, full: html, text
    tidying up description page
  • 1.5 lines changed: 2, context: html, text, full: html, text
    tidy up
  • 1.4 lines changed: 102, context: html, text, full: html, text
    adding links to pubmed and tidying up generally
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.7 lines changed: 20, context: html, text, full: html, text
    wrapping at 80 chars
  • 1.6 lines changed: 5, context: html, text, full: html, text
    adding TARGET to HREF
  • 1.5 lines changed: 4, context: html, text, full: html, text
    add contact
  • 1.4 lines changed: 56, context: html, text, full: html, text
    standardising text
• src/hg/utils/automation/Encode.pm
  • 1.35 lines changed: 7, context: html, text, full: html, text
    check if a file is a tar
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.17 lines changed: 18, context: html, text, full: html, text
    fixing to copy the kent src over to each new release because cvs-reports-d does a cvs update, not cvs checkout
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.50 lines changed: 3, context: html, text, full: html, text
    v202 final build