add test around having missing LB tags

integration-test/bam-readcount_test.py

@@ -70,20 +70,21 @@ def test_bamreadcount_normal_as_list(self):
         self.assertEqual(0, rv)
         self.assertFilesEqual(expected_file, output_file)
 
-    def test_bamreadcount_perlib(self):
-        """test per lib output is as expected"""
-        expected_file = "expected_per_lib"
-        bam_file = "test.bam"
+    def test_bamreadcount_when_lib_absent(self):
+        """test that we can run if there was no LB in the header"""
+        expected_file = "expected_all_lib"
+        bam_file = "test_bad_rg.bam"
         ref_fasta = "ref.fa"
-        site_list = "site_list"
+        regions = "21:10402985-10402985 21:10405200-10405200"
         output_file = self.tempFile("output")
-        cmdline = " ".join([self.exe_path, '-p', '-f', ref_fasta, '-l', site_list, bam_file, '>', output_file])
+        cmdline = " ".join([self.exe_path, '-f', ref_fasta, bam_file, regions, '>', output_file])
         print "Executing", cmdline
         print "CWD", os.getcwd()
         rv = subprocess.call(cmdline, shell=True)
         print "Return value:", rv
         self.assertEqual(0, rv)
-        self.assertFilesEqual(expected_file, output_file) 
+        self.assertFilesEqual(expected_file, output_file)
+
     def test_bamreadcount_indel_centric_normal(self):
         """test all lib output, but with insertion centric counting"""
         expected_file = "expected_insertion_centric_all_lib"