Mercurial > repos > jjohnson > snpeff
diff snpSift_filter.xml @ 5:192a236898f5
Add test cases for SnpSift
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 25 Mar 2013 08:51:33 -0500 |
| parents | fe23d90249ee |
| children | 13b6ad2ddace |
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--- a/snpSift_filter.xml Wed Mar 20 13:19:14 2013 -0500 +++ b/snpSift_filter.xml Mon Mar 25 08:51:33 2013 -0500 @@ -29,6 +29,59 @@ <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> + + <tests> + + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="QUAL >= 50"/> + <output name="output"> + <assert_contents> + <not_has_text text="25967" /> + <not_has_text text="NT_166464" /> + </assert_contents> + </output> + </test> + + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(CHROM = '19')"/> + <output name="output"> + <assert_contents> + <has_text text="3205820" /> + <not_has_text text="NT_16" /> + </assert_contents> + </output> + </test> + + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(POS >= 20175 & (POS <= 35549)"/> + <output name="output"> + <assert_contents> + <has_text text="20175" /> + <has_text text="35549" /> + <has_text text="22256" /> + <not_has_text text="18933" /> + <not_has_text text="37567" /> + </assert_contents> + </output> + </test> + + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="( DP >= 5 )"/> + <output name="output"> + <assert_contents> + <has_text text="DP=5;" /> + <has_text text="DP=6;" /> + <not_has_text text="DP=1;" /> + </assert_contents> + </output> + </test> + + </tests> + <help> **SnpSift filter**