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PartitionAndJoin should throw an exception if it sees an unmapped read #297
PartitionAndJoin crashes with a null pointer exception when I call it to join a set of 4 mouse-chrM coordinates with a small mouse file.
You can find my mouse.bam, mouse.adam, the coordinate test.txt file and my source code here:
This is the exception stack:
changed the title from
PartitionAndJoin should throw an exception if it sees an unmapped read
Oct 14, 2014
This was referenced
Oct 15, 2014
So the question here is, "should it throw an exception?" (which technically, it already does: it throws an un-interpretable NPE) Or "should it simply filter out the unmapped reads before attempting to do the join?"
I'm inclined to think that the latter is a better option.
I like the fast-fail exception but we should ensure that it's easy for a
On Wed, Oct 15, 2014 at 3:51 PM, Frank Austin Nothaft <