Mercurial > repos > jjohnson > pileup_to_vcf

changeset 5:8688e29ba96f

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Fix test 2
author Jim Johnson <jj@umn.edu>
date Tue, 19 Mar 2013 15:05:20 -0500
parents fafa105e5f58
children d90f56ecd2f9
files pileup_to_vcf.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/pileup_to_vcf.xml	Tue Mar 19 13:04:40 2013 -0500
+++ b/pileup_to_vcf.xml	Tue Mar 19 15:05:20 2013 -0500
@@ -92,7 +92,7 @@
     <test>
       <param name="input_file" ftype="pileup" value="test.pileup" />
       <param name="select_order" value="no"/>
-      <param name="min_base_qual" value="20"/>
+      <param name="min_base_qual" value="5"/>
       <param name="min_cvrg" value="5"/>
       <param name="min_var_pct" value=".1"/>
       <param name="allow_multiples" value="True"/>
@@ -101,7 +101,8 @@
       <output name="output_file">
         <assert_contents>
             <has_text_matching expression="seq2\t156\t.\tA\tG,AAG\t.\tPASS\t.*" />
-            <has_text_matching expression="chr1\t158571283\t.\tA\tC\t.\tPASS\t.*" />
+            <has_text_matching expression="chr1\t158571283\t.\tA\tT\t.\tPASS\t.*" />
+            <not_has_text text="125070485" />
         </assert_contents>
       </output>
     </test>