Changes

== Review Sept 20th ==

== Review Sept 20th ==

=== Notes ===

=== Notes ===

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 ===

</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.