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=== In Case You Are Curious ===
=== FAQ ===
This section contains information about what the filters mean, how they work, etc.
This section contains information about what the filters mean, how they work, etc.
'''What should the quality count as if the quality string is '*'?'''
'''What should the quality count as if the quality string is '*'?'''
:That is the purpose of the <code>defaultQualityInt</code> parameter.
:That is the purpose of the <code>defaultQualityInt</code> parameter.
'''Is the quality threshold or the clipping checked first?'''
:First the mismatch threshold is checked so clipping is performed. Then the quality threshold is checked on the non-clipped mismatches. That way mismatches that are clipped do not go into the sum of the mismatch qualities.
'''How is the quality threshold checked?'''
: Easy, just loop through an alignment finding mismatches. Add up the quality of the mismatches. If they sum is greater than the quality threshold, mark the read as unmapped.
'''How is the mismatch threshold checked?'''
: This is requires a bit more logic...
