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, 09:53, 21 March 2012
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| <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> | | <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> |
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| + | == Rules == |
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| + | '''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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