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Revision as of 12:01, 2 February 2017
, 12:01, 2 February 2017→Accessing String Values
[[Category:libStatGen]]
[[Category:libStatGen BAM]]
== Review Sept 20th ==
=== Notes ===
* returning const char*
* SamFileHeader change referenceContigs, etc to private from public
* Add way to copy a SAM record.
== Review Sept 17th ==
== Review Sept 17th ==
=== Topics Discussed ===
=== Topics Discussed ===
=== NOTES From Meeting ===
=== NOTES From Meeting ===
*InputFile should not use <code>long int</code>. Should instead use: <code>long long</code>
* General Notes:
*Anytime have an error could call handleError which would have a switch to return the error, throw exception, or abort. Call it with an error code and a string. Maybe an error handler class where you could use everywhere. Each class would have a member of that class type that would contain that information.
**InputFile should not use <code>long int</code>. Should instead use: <code>long long</code>
* Error Handling Notes:
**Anytime have an error could call handleError which would have a switch to return the error, throw exception, or abort. Call it with an error code and a string. Maybe an error handler class where you could use everywhere. Each class would have a member of that class type that would contain that information.
*Returning values of Strings Notes:
** Problems with returning const char*
*** If the pointer is stored when returned, it becomes invalid if the class modifies the underlying string.
** Problems with passing in std::string& as a parameter to be set.
*** people typically want to operate on the return of the method.
** One idea was returning a reference to a string
*** Does that solve the problem? Won't the contents change when a new one is read? Is that what we want?
=== Useful Links ===
BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs
BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs
Source Code: http://www.sph.umich.edu/csg/mktrost/doxygen/html/
Source Code: http://csg.sph.umich.edu//mktrost/doxygen/html/
Test code for setting values in the library: http://www.sph.umich.edu/csg/mktrost/doxygen/html/WriteFiles_8cpp-source.html
Test code for setting values in the library: http://csg.sph.umich.edu//mktrost/doxygen/html/WriteFiles_8cpp-source.html
=== Topics for Discussion ===
=== Topics for Discussion ===
return mySequence.c_str();
return mySequence.c_str();
}
}
const std::string& SamRecord::getSequence()
const char* SamRecord::getSequence(std::string& sequence)
{
{
myStatus = SamStatus::SUCCESS;
myStatus = SamStatus::SUCCESS;
// 0 Length, means that it is in the buffer, but has not yet
// 0 Length, means that it is in the buffer, but has not yet
// been synced to the string, so do the sync.
// been synced to the string, so do the sync.
setSequenceAndQualityFromBuffer(); // Can fail.
setSequenceAndQualityFromBuffer();
}
}
return &mySequence;
return mySequence.c_str();
}
}
</source>
</source>
and passing in references to strings, like:
and passing in references to strings, like:
</source>
</source>
http://www.sph.umich.edu/csg/mktrost/doxygen/html/SamRecord_8h-source.html
http://csg.sph.umich.edu//mktrost/doxygen/html/SamRecord_8h-source.html
==== SamFileHeader ====
==== SamFileHeader ====
** <S>include links from the main library page and the SamFile page.</s>
** <S>include links from the main library page and the SamFile page.</s>
** <S>look into why the one example have two if checks on SamIn status</s> <span style="color:blue">- one was printing the result and one was setting the return value - cleaned up to be in one if statement.</span>
** <S>look into why the one example have two if checks on SamIn status</s> <span style="color:blue">- one was printing the result and one was setting the return value - cleaned up to be in one if statement.</span>
* Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.
* <S>Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.</s>
** What should this library be called?
** <S>What should this library be called?</s> <span style="color:blue">- Created library: libstatgen and reorganized into a new repository: statgen.</span>
*** libdna
*** <S>libdna</s>
*** libdna++
*** <S>libdna++</s>
*** libsequence++
*** <S>libsequence++</s>
*** libDNA
*** <S>libDNA</s>
*** libgenotype
*** <S>libgenotype</s>
* 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.
