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* [[C++ Executable: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]
* [[C++ Executable: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]
* [[C++ Executable: bam#readReference|readReference - Print the reference string for the specified region]]
* [[C++ Executable: bam#readReference|readReference - Print the reference string for the specified region]]
* [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]]
This executable is built using [[StatGenLibrary: BAM]].
This executable is built using [[StatGenLibrary: BAM]].
The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]]
The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]]
== diff ==
<span style="color:#D2691E">'''***Coming Soon***'''</span>
The <code>diff</code> option on the bam executable prints the difference between two SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools.
=== Parameters ===
<pre>
Required Parameters:
--in1 : first SAM/BAM file to be diffed
--in2 : second SAM/BAM file to be diffed
Optional Parameters:
--seq : diff the sequence bases.
--baseQual : diff the base qualities.
--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--noCigar : do not diff the the cigars.
--noPos : do not diff the positions.
--onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed.
--recPoolSize : number of records to allow to be stored at a time, default value: 1000000
--posDiff : max base pair difference between possibly matching records100000
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
=== Usage ===
./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: an error occurred processing the parameters or reading one of the files.
=== Output Format ===
== readReference ==
== readReference ==
