From e35fa87fbd422d94bb4585f2f8d3cf8c6baae3f3 Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Thu, 30 Oct 2008 16:03:11 -0400
Subject: [PATCH] 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.

---
 tools/new_operations/complement.xml |  5 +++++
 tools/new_operations/coverage.xml   |  5 +++++
 tools/new_operations/intersect.xml  | 22 ++++++++++++++++++----
 tools/new_operations/merge.xml      |  5 +++++
 tools/new_operations/subtract.xml   |  7 +++++++
 5 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml
index 84ca368c712..be661ee6f4a 100644
--- a/tools/new_operations/complement.xml
+++ b/tools/new_operations/complement.xml
@@ -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" />
diff --git a/tools/new_operations/coverage.xml b/tools/new_operations/coverage.xml
index 63475e98fc5..979db1e6533 100644
--- a/tools/new_operations/coverage.xml
+++ b/tools/new_operations/coverage.xml
@@ -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" />
diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml
index a2975178c63..5a755548a42 100644
--- a/tools/new_operations/intersect.xml
+++ b/tools/new_operations/intersect.xml
@@ -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" />
diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml
index ce7a349292c..c0118db9d25 100644
--- a/tools/new_operations/merge.xml
+++ b/tools/new_operations/merge.xml
@@ -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" />
diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml
index 9a6ca6e3868..2a58e1654ee 100644
--- a/tools/new_operations/subtract.xml
+++ b/tools/new_operations/subtract.xml
@@ -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" />