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, 16:24, 30 September 2010
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| [bam_sort_core] merging from 3 files... | | [bam_sort_core] merging from 3 files... |
| </pre> | | </pre> |
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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. |
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| + | '''What should the quality count as if the quality string is '*'?''' |
| + | :That is the purpose of the <code>defaultQualityInt</code> parameter. |