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Merge branch 'master' into dev
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David Jones committed Mar 27, 2018
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* Recommend upgrading to [alleleCount v4.0.0+](https://github.com/cancerit/alleleCount/releases)
* Switches to fragment based counts instead of read based to prevent double counting.

## 4.1.2

* Updated tabix->query to use tabix->query_full

## 4.1.1

* Fix error in setup.sh testing of alleleCounter version
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