<commit_before><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.0">snpEff</requirement>
        </requirements>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
  </xml>
  <token name="@EXTERNAL_DOCUMENTATION@">

For details about this tool, please go to http://snpeff.sourceforge.net/ .

  </token>
  <token name="@CITATION_SECTION@">------

**Citation**

For the underlying tool, please cite the following two publications:

SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. Fly 6(2):80-92, 2012

SnpSift citation:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.

  </token>
  <xml name="citations">
      <citations>
        <citation type="doi">10.3389/fgene.2012.00035</citation>
        <citation type="doi">10.4161/fly.19695</citation>
        <yield />
      </citations>
  </xml>
</macros><commit_msg>update snpEff to version 4 and merge all changes from JJ, Nicola and Bjoern<commit_after><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.0">snpEff</requirement>
        </requirements>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
  </xml>
  <token name="@EXTERNAL_DOCUMENTATION@">

For details about this tool, please go to:
	http://snpeff.sourceforge.net/SnpEff_manual.html

  </token>
  <token name="@CITATION_SECTION@">------

**Citation**

For the underlying tool, please cite the following two publications:

SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. Fly 6(2):80-92, 2012

SnpSift citation:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", <NAME>., et. al., Frontiers in Genetics, 3:35, 2012.

  </token>
  <xml name="citations">
      <citations>
        <citation type="doi">10.3389/fgene.2012.00035</citation>
        <citation type="doi">10.4161/fly.19695</citation>
        <yield />
      </citations>
  </xml>
</macros>
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