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, 16:00, 31 January 2012
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| --storeOrig : Store the original cigar in the specified tag. | | --storeOrig : Store the original cigar in the specified tag. |
| --readName : Original file is sorted by Read Name instead of coordinate. | | --readName : Original file is sorted by Read Name instead of coordinate. |
| + | --stats : Print some statistics on the overlaps. |
| --noeof : Do not expect an EOF block on a bam file. | | --noeof : Do not expect an EOF block on a bam file. |
| --params : Print the parameter settings | | --params : Print the parameter settings |
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| If your file is sorted by read name rather than by coordinate, specify <code>--readName</code>. The resulting file will still be sorted by read name. | | If your file is sorted by read name rather than by coordinate, specify <code>--readName</code>. The resulting file will still be sorted by read name. |
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| + | == Print Overlap Statistics (<code>--stats</code>)== |
| + | Print some basic overlap statistics to stderr. |
| + | |
| + | Output values |
| + | * count of the number of overlapping pairs that are clipped |
| + | * average of the number of overlapping reference bases that are clipped |
| + | * variance of the number of overlapping reference bases that are clipped |
| + | * number of times the forward strand is clipped when read pairs overlap |
| + | * number of times the reverse strand is clipped when read pairs overlap |
| + | * number of times the orientation causes clipping/additional clipping |
| + | ** reads that are only clipped due to orientation are not counted in the other stats |
| + | |
| + | |
| + | === Example Output === |
| + | <pre> |
| + | Overlap Statistics: |
| + | Number of overlapping pairs: 14 |
| + | Average # Reference Bases Overlapped: 18.3571 |
| + | Variance of Reference Bases overlapped: 39.1703 |
| + | Number of times the forward strand was clipped: 6 |
| + | Number of times the reverse strand was clipped: 8 |
| + | Number of times orientation causes additional clipping: 4 |
| + | </pre> |
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