BAM Review Action Items

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Revision as of 08:36, 17 September 2010 by Mktrost (talk | contribs)
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Review Sept 17th

Review June 7th

  • Move the examples from the SamFile wiki page to their own page
    • include links from the main library page and the SamFile page.
    • look into why the one example have two if checks on SamIn status - one was printing the result and one was setting the return value - cleaned up to be in one if statement.
  • Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.
    • What should this library be called?
      • libdna
      • libdna++
      • libsequence++
      • libDNA
      • libgenotype
  • Add an option by class that says whether or not to abort on failure. (or even an option on each method)
    • This allows calling code to set that option and then not have to check for failures since the code it calls would abort on a failure.
    • Could/should this be achieved using exceptions? User can decide to catch them or let them terminate the program.
  • SamFile add a constructor that takes the filename and a flag to indicate open for read/write. (abort on failure to open)
    • Also have 2 subclasses one that opens for read, one for write: SamReadFile, SamWriteFile? Or SamFileRead, SamFileWrite? - went with SamFileReader and SamFileWriter
  • Add a function that says: skipInvalidRecords, validateRecords, etc.
    • That way, ReadRecord will keep reading records until a valid/parseable one is found.
  • SamFileHeader::setTag - instead of having separate ones for PG, RG, etc, have a generic one that takes as a parameter which one it is.
    • KeyID, then Value as parameters....(keyID first, then value)
  • SamFileHEader::setProgramName, etc...have specific methods for setting fields so users don't need to know the specific tags, etc used for certain values in the header.
    • KeyID, then Value as parameters....(keyID first, then value)
  • BAM write utility could add a PG field with default settings (user could specify alternate settings) when it writes a file.
  • Future methods to add:
    • SamFile::setReadSection(const std::string& refName) - take in the reference name by string since that is what most people will know.
      • "" would indicate the ones not associated with a reference.