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Revision as of 17:28, 9 December 2010
, 17:28, 9 December 2010no edit summary
** <code>BamInterface::writeRecord</code> passes the translation parameter to <code>SamRecord::writeRecordBuffer</code>
** <code>BamInterface::writeRecord</code> passes the translation parameter to <code>SamRecord::writeRecordBuffer</code>
** <code>SamInterface::writeRecord</code> passes the translation parameter to <code>SamRecord::getSequence</code> when it obtains the sequence to write into the SAM file.
** <code>SamInterface::writeRecord</code> passes the translation parameter to <code>SamRecord::getSequence</code> when it obtains the sequence to write into the SAM file.
=== FAQ ===
'''Q: How do you know what the actual base was? Doesn't that depend on the specific reference used to do the alignment'''
A: The user needs to create a <code>GenomeSequence</code> object, specifying the fasta file. That object is used to map to the reference.
'''Q: What if I don't know what my reference file is?'''
A: Then I don't either. Although....additional validation will be added to check the reference specified versus the SQ fields in the header: [[BAM Convert Sequences#STILL NEEDS WORK|Additional Validation Coming Soon]]
=== STILL NEEDS WORK ===
*Additional validation will be added to check the specified GenomeSequence against the Header from the SamFile. It will check things like sequence length. An error will be reported if the reference sequence length does not match the SQ LN field for that reference name. This will give you an indication of if you are using the wrong reference file.
