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BamUtil: filter

698 bytes added, 15:24, 30 September 2010
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[bam_sort_core] merging from 3 files...
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=== In Case You Are Curious ===
This section contains information about what the filters mean, how they work, etc.
 
'''What counts as a match or a mismatch?'''
:Only bases with a cigar values of M, X, or = can be counted as matches or mismatches. Cigar I, D, N, S, P, and H are NOT matches or mismatches.
:If either the reference or the read are 'N' or 'n', it is NOT a match or mismatch.
:It is a match if the reference and the read have the same base (both A/a, both C/c, both G/g, or both T/t). If they are different, non-'N', bases it is a mismatch.
 
'''What should the quality count as if the quality string is '*'?'''
:That is the purpose of the <code>defaultQualityInt</code> parameter.

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