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637 bytes added
, 15:55, 30 September 2010
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the SAM/BAM file to be read
| + | --in : the SAM/BAM file to be read |
− | --refFile : the reference file
| + | --refFile : the reference file |
− | Optional Parameters:
| + | --out : the SAM/BAM file to write to |
− | --noeof : do not expect an EOF block on a bam file.
| + | 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> [--noeof]
| + | ./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] |
| | | |
| === Return Value === | | === Return Value === |