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BAM Review Action Items (view source)

Revision as of 13:43, 17 September 2010

251 bytes added ,  13:43, 17 September 2010
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=== Review Sept 17th ===
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== Review Sept 17th ==
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=== Topics Discussed ===
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* [[#Return Statuses|Checking if methods succeeded/failed (checking return values/return statuses)]]
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* [[#Accessing String Values|Strings as return values]]
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=== NOTES From Meeting ===
 
*InputFile should not use <code>long int</code>.  Should instead use: <code>long long</code>
 
*InputFile should not use <code>long int</code>.  Should instead use: <code>long long</code>
 
*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.
 
*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.
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==== Review Discussion Topics ====
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==== Useful Links ====
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http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs
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BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs
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Source Code: http://www.sph.umich.edu/csg/mktrost/doxygen/html/
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http://www.sph.umich.edu/csg/mktrost/doxygen/html/
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Test code for setting values in the library: http://www.sph.umich.edu/csg/mktrost/doxygen/html/WriteFiles_8cpp-source.html
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Example of using the library to set values: http://www.sph.umich.edu/csg/mktrost/doxygen/html/WriteFiles_8cpp-source.html
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=== Topics for Discussion ===
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===== Return Statuses =====
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==== 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">
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===== Accessing String Values =====
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==== 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?
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http://www.sph.umich.edu/csg/mktrost/doxygen/html/SamRecord_8h-source.html
 
http://www.sph.umich.edu/csg/mktrost/doxygen/html/SamRecord_8h-source.html
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===== SamFileHeader =====
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==== 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?
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Should these also be added to SamHeaderRG, SamHeaderSQ, etc as appropriate....
 
Should these also be added to SamHeaderRG, SamHeaderSQ, etc as appropriate....
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=== Review June 7th ===
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== 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>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2036"

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