75
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add new name options, spelling corrections
** include links from the main library page and the SamFile 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
** 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.
* Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.
** What should this library be called?
** What should this library be called?
*** libdna
*** libdna
*** libdna++
*** libdna++
*** libsequence++
*** libsequence++
*** libDNA
*** libgenotype
* Add an option by class that says whether or not to abort on failure. (or even an option on each method)
* 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.
** 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.
** Also have 2 subclasses one that opens for read, one for write: SamReadFile, SamWriteFile? Or SamFileRead, SamFileWrite?
** 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.
* Add a function that says: skipInvalidRecords, validateRecords, etc.
** That way, ReadRecord will keep reading records until a valid/parsable one is found.
** That way, ReadRecord will keep reading records until a valid/parseable 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.
*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)
** 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.
* 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.
