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Returns the SamStatus for the reads/writes. 0 on success.
Returns the SamStatus for the reads/writes. 0 on success.
= Example Output =
= Examples =
==Trim the same number of bases from each side==
Example Input, trimming 2 bases:
<pre>
./bin trimBam testFiles/testSam.sam results/trimSam.sam 2
</pre>
Example Output:
<pre>
<pre>
Arguments in effect:
Arguments in effect:
</pre>
</pre>
==Trim different bases from each side, but treat forward & reverse the same==
Example Input, trimming 1 base from the left and 2 bases from the right:
<pre>
./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2
</pre>
Example Output:
<pre>
<pre>
Arguments in effect:
Arguments in effect:
==Trim different bases from each side, but treat reverse strands the opposite==
Example Input, trimming 1 base from the left and 2 bases from the right for forward strands and do the opposite for reverse strands:
<pre>
./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --reverse
</pre>
Example Output:
<pre>
<pre>
Arguments in effect:
Arguments in effect:
