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Revision as of 10:16, 17 September 2010
, 10:16, 17 September 2010no edit summary
=== Review Sept 17th ===
=== Review Sept 17th ===
==== Review Discussion Topics ====
==== Review Discussion Topics ====
http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs
http://www.sph.umich.edu/csg/mktrost/doxygen/html/
Example of using the library to set values: http://www.sph.umich.edu/csg/mktrost/doxygen/html/WriteFiles_8cpp-source.html
===== Return Statuses =====
===== 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:
Aborted
Aborted
</pre>
</pre>
===== Accessing String Values =====
SAM/BAM files have strings in them that people will want to read out.
How should we handle this interface?
Currently we do a mix of returning const char*, like:
<source lang="cpp">
const char* 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.c_str();
}
</source>
and passing in references to strings, like:
<source lang="cpp">
// Set the passed in string to the header line at the specified index.
// It does NOT clear the current contents of header.
// NOTE: some indexes will return blank if the entry was deleted.
bool SamFileHeader::getHeaderLine(unsigned int index, std::string& header) const
{
// Check to see if the index is in range of the header records vector.
if(index < myHeaderRecords.size())
{
// In range of the header records vector, so get the string for
// that record.
SamHeaderRecord* hdrRec = myHeaderRecords[index];
hdrRec->appendString(header);
return(true);
}
else
{
unsigned int commentIndex = index - myHeaderRecords.size();
// Check to see if it is in range of the comments.
if(commentIndex < myComments.size())
{
// It is in range of the comments, so add the type.
header += "@CO\t";
// Add the comment.
header += myComments[commentIndex];
// Add the new line.
header += "\n";
return(true);
}
}
// Invalid index.
return(false);
}
</source>
http://www.sph.umich.edu/csg/mktrost/doxygen/html/SamRecord_8h-source.html
===== SamFileHeader =====
===== 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 we add the following to SamFileHeader:
<source lang="cpp">
//////////////////////////////////
// Set methods for header fields.
bool setVersion(const char* version);
bool setSortOrder(const char* sortOrder);
bool addSequenceName(const char* sequenceName);
bool setSequenceLength(const char* keyID, int sequenceLength);
bool setGenomeAssemblyId(const char* keyID, const char* genomeAssemblyId);
bool setMD5Checksum(const char* keyID, const char* md5sum);
bool setURI(const char* keyID, const char* uri);
bool setSpecies(const char* keyID, const char* species);
bool addReadGroupID(const char* readGroupID);
bool setSample(const char* keyID, const char* sample);
bool setLibrary(const char* keyID, const char* library);
bool setDescription(const char* keyID, const char* description);
bool setPlatformUnit(const char* keyID, const char* platform);
bool setPredictedMedianInsertSize(const char* keyID, const char* isize);
bool setSequencingCenter(const char* keyID, const char* center);
bool setRunDate(const char* keyID, const char* runDate);
bool setTechnology(const char* keyID, const char* technology);
bool addProgram(const char* programID);
bool setProgramVersion(const char* keyID, const char* version);
bool setCommandLine(const char* keyID, const char* commandLine);
///////////////////////////////////
// Get methods for header fields.
// Returns the number of SQ entries in the header.
int32_t getSequenceDictionaryCount();
// Return the Sort Order value that is set in the Header.
// If this field does not exist, "" is returned.
const char* getSortOrder();
/// Additional gets for the rest of the fields.
</source>
Should these also be added to SamHeaderRG, SamHeaderSQ, etc as appropriate....
=== Review June 7th ===
=== Review June 7th ===
