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BamUtil: asp

676 bytes added, 08:53, 21 March 2012
Update rules used for creating the ASP
<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
 
 
== Rules ==
 
'''Dealing with 'N' Bases'''
* If the reference is 'N':
** Do Not write REF_ONLY or DETAILED records
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If all reads at this position are 'N':
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If some reads are 'N' and the rest are the reference (not 'N')
** Write a REF_ONLY record but do not include the 'N's in the numBases
* If some reads are 'N' and some are non-reference (not 'N')
** DEFAULT: Write a DETAILED record and include the 'N's in the numBases
** OPTIONAL: Write a DETAILED record but do not include the 'N's in the numBases

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