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comparison snpSift_filter.xml @ 5:192a236898f5

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Add test cases for SnpSift
author Jim Johnson <jj@umn.edu>
date Mon, 25 Mar 2013 08:51:33 -0500
parents fe23d90249ee
children 13b6ad2ddace
comparison
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4:fe23d90249ee 5:192a236898f5
27 </outputs> 27 </outputs>
28 <stdio> 28 <stdio>
29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
30 <exit_code range="1:" level="fatal" description="Error" /> 30 <exit_code range="1:" level="fatal" description="Error" />
31 </stdio> 31 </stdio>
32
33 <tests>
34
35 <test>
36 <param name="input" ftype="vcf" value="test01.vcf"/>
37 <param name="expr" value="QUAL >= 50"/>
38 <output name="output">
39 <assert_contents>
40 <not_has_text text="25967" />
41 <not_has_text text="NT_166464" />
42 </assert_contents>
43 </output>
44 </test>
45
46 <test>
47 <param name="input" ftype="vcf" value="test01.vcf"/>
48 <param name="expr" value="(CHROM = '19')"/>
49 <output name="output">
50 <assert_contents>
51 <has_text text="3205820" />
52 <not_has_text text="NT_16" />
53 </assert_contents>
54 </output>
55 </test>
56
57 <test>
58 <param name="input" ftype="vcf" value="test01.vcf"/>
59 <param name="expr" value="(POS >= 20175 & (POS <= 35549)"/>
60 <output name="output">
61 <assert_contents>
62 <has_text text="20175" />
63 <has_text text="35549" />
64 <has_text text="22256" />
65 <not_has_text text="18933" />
66 <not_has_text text="37567" />
67 </assert_contents>
68 </output>
69 </test>
70
71 <test>
72 <param name="input" ftype="vcf" value="test01.vcf"/>
73 <param name="expr" value="( DP >= 5 )"/>
74 <output name="output">
75 <assert_contents>
76 <has_text text="DP=5;" />
77 <has_text text="DP=6;" />
78 <not_has_text text="DP=1;" />
79 </assert_contents>
80 </output>
81 </test>
82
83 </tests>
84
32 <help> 85 <help>
33 86
34 **SnpSift filter** 87 **SnpSift filter**
35 88
36 You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility. 89 You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.