Update test_junctions_extract.py

Author: kcotto

tests/integration-test/test_junctions_extract.py

@@ -39,7 +39,7 @@ def test_junctions_extract_anchor_stranded(self):
                                             anchor + ".out")[0]
             if anchor != "":
                 anchor = "-a " + anchor
-            params = ["junctions", "extract", anchor, "-s 1", "-o", output_file, bam1]
+            params = ["junctions", "extract", anchor, "-s RF", "-o", output_file, bam1]
             rv, err = self.execute(params)
             self.assertEqual(rv, 0)
             self.assertFilesEqual(expected_file, output_file)
@@ -53,7 +53,7 @@ def test_junctions_extract_anchor(self):
                                             anchor + ".out")[0]
             if anchor != "":
                 anchor = "-a " + anchor
-            params = ["junctions", "extract", anchor, "-s 0", "-o", output_file, bam1]
+            params = ["junctions", "extract", anchor, "-s XS", "-o", output_file, bam1]
             rv, err = self.execute(params)
             self.assertEqual(rv, 0)
             self.assertFilesEqual(expected_file, output_file)
@@ -66,7 +66,7 @@ def test_junctions_extract_intron_size(self):
         expected_file = self.inputFiles("junctions-extract/expected-i" +
                 min_intron + "-I" + max_intron +
                 ".out")[0]
-        params = ["junctions", "extract", "-s 0", "-o", output_file,
+        params = ["junctions", "extract", "-s XS", "-o", output_file,
                   "-m", min_intron, "-M", max_intron, bam1]
         rv, err = self.execute(params)
         self.assertEqual(rv, 0)
@@ -78,21 +78,21 @@ def test_region(self):
         region = "1:22405013-22405020"
         expected_file = self.inputFiles("junctions-extract/expected-r" +
                 region + ".out")[0]
-        params = ["junctions", "extract", "-s 0", "-o", output_file, "-r", region,
+        params = ["junctions", "extract", "-s XS", "-o", output_file, "-r", region,
                   bam1]
         rv, err = self.execute(params)
         self.assertEqual(rv, 0)
         self.assertFilesEqual(expected_file, output_file)
 
     def test_no_bam(self):
         output_file = self.tempFile("extract.out")
-        params = ["junctions", "extract", "-s 0", "-o", output_file]
+        params = ["junctions", "extract", "-s XS", "-o", output_file]
         rv, err = self.execute(params)
         self.assertEqual(rv, 1)
 
     def test_missing_bam(self):
         output_file = self.tempFile("extract.out")
-        params = ["junctions", "extract", "-s 0", "-o", output_file, "does_not_exist.bam"]
+        params = ["junctions", "extract", "-s XS", "-o", output_file, "does_not_exist.bam"]
         rv, err = self.execute(params)
         self.assertEqual(rv, 1)