BAM Review Action Items

• 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
• Create 1 library for all of our library code rather than having libcsg, libbam, libfqf seperated.
  • What should this library be called?
    • libdna
    • libdna++
    • libsequence++
• 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.
  • Also takes a flag to indicate open for read/write.
  • Also have 2 subclasses one that opens for read, one for write: SamReadFile, SamWriteFile? Or SamFileRead, SamFileWrite?
• Add a function that says: skipInvalidRecords, validateRecords, etc.
  • That way, ReadRecord will keep reading records until a valid/parsable one is found.
• SamFileHeader::setTag - instead of having sepearate 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.