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[[Category:libbam]]
== filter ==
The <code>filter</code> option on the [[Bam|bam executable]] writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high.
=== Parameters ===
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--refFile : the reference file
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
</pre>
=== Usage ===
./bam filter --in <inputFilename> --refFile <referenceFilename> [--noeof]
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
=== Example Output ===
<pre>
The following parameters are available. Ones with "[]" are in effect:
Input Parameters
--in [testFiles/testFilter.sam], --out [-],
--refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold [30],
--defaultQualityInt [20], --mismatchThreshold [0.49]
open and prefetch reference genome testFiles/chr1_partial.fa: done.
Number of Reads Clipped by Filtering: 8
Number of Reads Filtered Due to MismatchThreshold: 1
Number of Reads Filtered Due to QualityThreshold: 2
</pre>
== filter ==
The <code>filter</code> option on the [[Bam|bam executable]] writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high.
=== Parameters ===
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--refFile : the reference file
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
</pre>
=== Usage ===
./bam filter --in <inputFilename> --refFile <referenceFilename> [--noeof]
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
=== Example Output ===
<pre>
The following parameters are available. Ones with "[]" are in effect:
Input Parameters
--in [testFiles/testFilter.sam], --out [-],
--refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold [30],
--defaultQualityInt [20], --mismatchThreshold [0.49]
open and prefetch reference genome testFiles/chr1_partial.fa: done.
Number of Reads Clipped by Filtering: 8
Number of Reads Filtered Due to MismatchThreshold: 1
Number of Reads Filtered Due to QualityThreshold: 2
</pre>
