Merge pull request #371 from AdamaJava/qprofiler_options

refactor(qprofiler2): add bad option check for longread

Author: newellf

qprofiler2/src/org/qcmg/qprofiler2/QProfiler2.java

@@ -99,6 +99,10 @@ protected int engage() throws Exception {
 				index = cmdLineIndexFiles[i];
 			}
 			ProfileType type = ProfileType.getType2(f);
+			if (type != ProfileType.BAM & isLongReadBam) {
+				   throw new Exception( Messages.getMessage(msgResource, "FILE_TYPE_LONG_READ_ERROR"));
+		    }
+
 			sortedFiles.computeIfAbsent(type, v -> new ArrayList<>()).add(Pair.of(f, index));
 		}		
 

qprofiler2/src/org/qcmg/qprofiler2/messages.properties

@@ -29,3 +29,4 @@ DATA_RECORD_ERROR = Data Record is null, or starts with an invalid character
 ID_RECORD_ERROR = ID Record is null, or starts with an invalid character
 OUTPUT_FILE_WRITE_ERROR = Cannot write to specified output file
 INPUT_FILE_ERROR = Cannot read supplied input file {0}
+FILE_TYPE_LONG_READ_ERROR = Long read option can only be chosen for BAM files

qprofiler2/test/org/qcmg/qprofiler2/QProfiler2Test.java

@@ -130,6 +130,25 @@ public final void executeWithInvalidFileType() throws Exception {
         }
     }
 
+    @Test
+    public final void executeWithInvalidFileTypeAndLongReadOption() throws Exception {
+                File gffFile = testFolder.newFile("executeWithInvalidFileTypeLongRead.vcf");
+                File logFile = testFolder.newFile("executeWithInvalidFileTypeLongRead.log");
+                File inputFile = testFolder.newFile("executeWithInvalidFileTypeLongRead.xml");
+
+                String[] args1 = {"-input", inputFile.getAbsolutePath(), "-log", logFile.getAbsolutePath(), "--long-read"};
+                String[] args2 = new String[]{"-input", gffFile.getAbsolutePath(), "-log", logFile.getAbsolutePath(), "--long-read"};
+
+                for (String[] args : new String[][]{args1, args2}) {
+                try {
+                    new QProfiler2().setup(args);
+                    fail("Should have thrown a QProfilerException");
+                } catch (Exception qpe) {
+                    assertTrue(qpe.getMessage().contains("Long read option can only be chosen for BAM files"));
+                }
+            }
+    }
+
     @Test
     public void schmeFileTest() throws IOException {
         String nameSpace = "https://adamajava.org/xsd/qprofiler2/v3";