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* 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.
** 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.
