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=== Parameters ===
=== Parameters ===
<pre>
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--refFile : the reference file
--out : the SAM/BAM file to write to
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--qualityThreshold : maximum sum of the mismatch qualities before marking
a read unmapped. (Defaults to 60)
--defaultQualityInt : quality value to use for mismatches that do not have a quality
(Defaults to 20)
--mismatchThreshold : decimal value indicating the maximum ration of mismatches to
matches and mismatches allowed before clipping from the ends
(Defaults to .10)
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>]
=== Return Value ===
=== Return Value ===
