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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
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.
== 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>
