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Samtools #101

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necrolyte2
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This is #72. It can be merged. Not using it right now, but may come into use later, see #66.
Also it includes a fix for vcfcat.

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I think the code needs to be restructured and all the assert statements should be pulled out and put into tests file

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Agreed. This is a bit of a mess, I'll do that as I fix the merge conflicts.

@averagehat averagehat self-assigned this Mar 17, 2016
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