96
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchBAM Review Action Items (view source)
Revision as of 12:01, 2 February 2017
, 12:01, 2 February 2017→Accessing String Values
[[Category:libStatGen]]
[[Category:libStatGen BAM]]
==== Review Discussion Topics ====
== 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 ==
=== Topics Discussed ===
* [[#Return Statuses|Checking if methods succeeded/failed (checking return values/return statuses)]]
* [[#Accessing String Values|Strings as return values]]
=== NOTES From Meeting ===
===== Return Statuses =====
* General Notes:
**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
Source Code: http://csg.sph.umich.edu//mktrost/doxygen/html/
Test code for setting values in the library: http://csg.sph.umich.edu//mktrost/doxygen/html/WriteFiles_8cpp-source.html
=== Topics for Discussion ===
==== Return Statuses ====
Currently anytime you do anything on a SAM/BAM file, you have to check the status for failure:
Currently anytime you do anything on a SAM/BAM file, you have to check the status for failure:
<source lang="cpp">
<source lang="cpp">
==== Accessing String Values ====
SAM/BAM files have strings in them that people will want to read out.
SAM/BAM files have strings in them that people will want to read out.
How should we handle this interface?
How should we handle this interface?
return mySequence.c_str();
return mySequence.c_str();
}
}
const std::string& SamRecord::getSequence()
{
myStatus = SamStatus::SUCCESS;
if(mySequence.Length() == 0)
{
// 0 Length, means that it is in the buffer, but has not yet
// been synced to the string, so do the sync.
setSequenceAndQualityFromBuffer();
}
return &mySequence;
}
</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 ====
*Should this be renamed to SamHeader?
*Should this be renamed to SamHeader?
*Do we like the classes being named starting with Sam? Should it be Bam?
*Do we like the classes being named starting with Sam? Should it be Bam?
Should these also be added to SamHeaderRG, SamHeaderSQ, etc as appropriate....
Should these also be added to SamHeaderRG, SamHeaderSQ, etc as appropriate....
== Review June 7th ==
* <S>Move the examples from the SamFile wiki page to their own page</s>
* <S>Move the examples from the SamFile wiki page to their own page</s>
** <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.
