File Changes for cline

v246_base to v247_preview (2011-01-25 to 2011-02-01) v247

• python/ucscgenomics/rafile/radict.pyc
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    Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 7, context: html, text, full: html, text
    Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
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    Added a bit more testing, revised the access of the exoniphy table to account for the fact that it no longer has a numeric ID. Fortunately, it doesn't look like that ID was used for anything
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 19, context: html, text, full: html, text
    Addressing Katrina's code review feedback
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    Changing the genders of several cell lines, in response to feedback from Terry Furey at Duke via Tim
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    Updated the validation documents for a slew of Myers lab antibodies
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    Added a stub cell growth 'protocol' for the prostate tissue. There was no cell growth protocol previously because no cells were grown: the RNA was purchased from a vendor. But, we need to have a protocol in place for the GEO submissions.
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    Updated the validation types of several Myers lab antibodies
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    Set the genders of several cell lines to Both, following word from Terry Furey that these cell lines consist of a mixture of both male and female cells
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 192, context: html, text, full: html, text
    Copying a bunch of changes from alpha to beta
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 11, context: html, text, full: html, text
    At Jim's suggestion, revised mostOverlappingBed so that if there is a bed of compatible gene structure, it will be chosen, but if there isn't such a bed, then some bed will still be chosen
• src/hg/txGene/txGeneValidation/checkRandomLinesExist.py
  • lines changed 40, context: html, text, full: html, text
    Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
  • lines changed 8, context: html, text, full: html, text
    Made the grep commands in this script prepared for some regular expression characters
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    Removed an extraneous diagnostic statement, and abandoned the idea of escaping special characters. The calling program is responsible for taking care of grep special characters
• src/hg/txGene/txGeneValidation/compareRandomSample.py
  • lines changed 40, context: html, text, full: html, text
    Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
• src/hg/txGene/txGeneValidation/makefile
  • lines changed 6, context: html, text, full: html, text
    Revised the makefile to play more nicely by copying the scripts to the directory, and removing its scripts from that directory prior to copying