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== Testing the build ==
== Testing the build ==
To test karma, go to the subdirectory named karma, and type the command:
make test
The test script builds a reference for the small phiX genome, then runs single end as well as paired end alignments. It compares the results of that with known results. Differences are printed to the console, and currently look something like this:
<pre>
diff phiX.sam.good phiX.sam
3c3
< @RG DT:2010-04-08T17:29Z ID:boingboing SM:NA12345
---
> @RG DT:2010-04-08T18:13Z ID:boingboing SM:NA12345
</pre>
= Normal Workflow =
= Normal Workflow =
