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Added new functional tests to all gops tools using BitsetSafeReaderWrapper. These tests check cases where datasets have the chr,start and end values in non-standard columns.

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This commit is contained in:
Guruprasad Anada
2008-10-30 16:03:11 -04:00
parent aeaf3c8978
commit e35fa87fbd
5 changed files with 40 additions and 4 deletions
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tools/new_operations/complement.xml
+5
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@@ -18,6 +18,11 @@
<param name="allchroms" value="true" />
<output name="output" file="gops_complement_out.bed" />
</test>
<test>
<param name="input1" value="2_mod.bed" ftype="interval"/>
<param name="allchroms" value="true" />
<output name="output" file="gops_complement_out_diffCols.dat" />
</test>
<test>
<param name="input1" value="gops_bigint.interval" />
<param name="allchroms" value="true" />
tools/new_operations/coverage.xml
+5
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@@ -19,6 +19,11 @@
<param name="input2" value="2.bed" />
<output name="output" file="gops_coverage_out.interval" />
</test>
<test>
<param name="input1" value="1.bed" />
<param name="input2" value="2_mod.bed" ftype="interval"/>
<output name="output" file="gops_coverage_out_diffCols.interval" />
</test>
<test>
<param name="input1" value="gops_bigint.interval" />
<param name="input2" value="gops_bigint2.interval" />
tools/new_operations/intersect.xml
+18 -4
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@@ -21,13 +21,27 @@
<data format="input" name="output" metadata_source="input1" />
</outputs>
<code file="operation_filter.py"/>
<tests>
<tests>
<test>
<param name="input1" value="1.bed" />
<param name="input2" value="2.bed" />
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops_intersect_out.bed" />
</test>
<test>
<param name="input1" value="1.bed" />
<param name="input2" value="2.bed" />
<param name="input2" value="2_mod.bed" ftype="interval"/>
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops_intersect_out.bed" />
<param name="returntype" value="" />
<output name="output" file="gops_intersect_diffCols.bed" />
</test>
<test>
<param name="input1" value="1.bed" />
<param name="input2" value="2_mod.bed" ftype="interval"/>
<param name="min" value="1" />
<param name="returntype" value="Overlapping pieces of Intervals" />
<output name="output" file="gops_intersect_p_diffCols.bed" />
</test>
<test>
<param name="input1" value="1.bed" />
tools/new_operations/merge.xml
+5
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@@ -21,6 +21,11 @@
<output name="output" file="gops-merge.dat" />
<param name="returntype" value="true" />
</test>
<test>
<param name="input1" value="2_mod.bed" ftype="interval"/>
<output name="output" file="gops_merge_diffCols.dat" />
<param name="returntype" value="true" />
</test>
<test>
<param name="input1" value="gops_bigint.interval" />
<output name="output" file="gops_merge_out2.bed" />
tools/new_operations/subtract.xml
+7
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@@ -32,6 +32,13 @@
<param name="returntype" value="" />
<output name="output" file="gops-subtract.dat" />
</test>
<test>
<param name="input1" value="1.bed" />
<param name="input2" value="2_mod.bed" ftype="interval"/>
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops_subtract_diffCols.dat" />
</test>
<test>
<param name="input1" value="gops_subtract_bigint.bed" />
<param name="input2" value="2.bed" />