kate: changes by file

branch to review (2010-03-02 to 2010-03-16) v227

• src/hg/encode/DAFs/2.0/:n
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    Pipeline 2.0
• src/hg/encode/DAFs/2.0/affyRnaChip.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • 1.1 lines changed: 40, context: html, text, full: html, text
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• src/hg/encode/DAFs/2.0/broadMapability.daf
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• src/hg/encode/DAFs/2.0/buOrchid.daf
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• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
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• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
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• src/hg/encode/DAFs/2.0/cshlRnaSeq.daf
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• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
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• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
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• src/hg/encode/DAFs/2.0/dukeExonArray.daf
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• src/hg/encode/DAFs/2.0/gisDnaPet.daf
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• src/hg/encode/DAFs/2.0/gisRnaPet.daf
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• src/hg/encode/DAFs/2.0/gisRnaSeq.daf
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• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • 1.1 lines changed: 42, context: html, text, full: html, text
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• src/hg/encode/DAFs/2.0/haibCnv.daf
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• src/hg/encode/DAFs/2.0/haibMethyl27.daf
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• src/hg/encode/DAFs/2.0/haibMethylSeq.daf
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• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
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• src/hg/encode/DAFs/2.0/helicosRnaSeq.daf
  • 1.1 lines changed: 54, context: html, text, full: html, text
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• src/hg/encode/DAFs/2.0/nhgriElnitskiBiPro.daf
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• src/hg/encode/DAFs/2.0/nhgriElnitskiNegReg.daf
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• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
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• src/hg/encode/DAFs/2.0/sangerGencode.daf
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• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
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• src/hg/encode/DAFs/2.0/stanfordRnaSeq.daf
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• src/hg/encode/DAFs/2.0/sunyRipChip.daf
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• src/hg/encode/DAFs/2.0/uMassDekker5c.daf
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• src/hg/encode/DAFs/2.0/uMassWengTfbsValid.daf
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• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
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• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
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• src/hg/encode/DAFs/2.0/uwChipSeq.daf
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• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
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• src/hg/encode/DAFs/2.0/uwDnaseValid.daf
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• src/hg/encode/DAFs/2.0/uwExonArray.daf
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    Pipeline 2.0
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.27 lines changed: 32, context: html, text, full: html, text
    Add compositeSuffix. Also some edits for readability.
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.14 lines changed: 61, context: html, text, full: html, text
    Merge in wrangler email (will obsolete labs.ra). Add some new labs and remove some aliases to retire
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.10 lines changed: 12, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Update for DAF 2.0
• src/hg/utils/automation/Encode.pm
  • 1.57 lines changed: 1, context: html, text, full: html, text
    Tweak error msg
  • 1.56 lines changed: 33, context: html, text, full: html, text
    Update DAF version to 2.0, freeze to June 2010, assemblies to hg19 and mm9, table/file name prefix to 'enc'. Add warning for beta testing.