PrintBGZFBlockInformation: remove file extension check so that we can…

… accept, eg., bams The file extension check in this tool was redundant, since there is a subsequent check that the input file is in BGZF format. Resolves #5800
broadinstitute · Mar 15, 2019 · 6161839 · 6161839
1 parent 811e72a
commit 6161839
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diff --git a/src/main/java/org/broadinstitute/hellbender/tools/PrintBGZFBlockInformation.java b/src/main/java/org/broadinstitute/hellbender/tools/PrintBGZFBlockInformation.java
@@ -71,11 +71,6 @@ protected void onStartup() {
             throw new UserException.CouldNotReadInputFile("File " + bgzfPathString + " does not exist");
         }
 
-        if ( ! IOUtil.hasBlockCompressedExtension(bgzfPathString) ) {
-            throw new UserException.CouldNotReadInputFile("File " + bgzfPathString + " does not end in a recognized BGZF file extension (" +
-                    StringUtils.join(IOUtil.BLOCK_COMPRESSED_EXTENSIONS, ",") + ")");
-        }
-
         try {
             // Check that the file is in BGZF format. This catches the "regular GZIP" case as well:
             if ( ! IOUtil.isBlockCompressed(bgzfPath) ) {

diff --git a/...st/java/org/broadinstitute/hellbender/tools/PrintBGZFBlockInformationIntegrationTest.java b/...st/java/org/broadinstitute/hellbender/tools/PrintBGZFBlockInformationIntegrationTest.java
@@ -100,4 +100,20 @@ public void testRegularGzipFile() throws IOException {
         };
         runCommandLine(args);
     }
+
+    /* Make sure that we can handle a standard BAM file */
+    @Test
+    public void testBamFile() throws IOException {
+        final File input = new File(packageRootTestDir + "engine/reads_data_source_test1.bam");
+        final File actualOutput = createTempFile("PrintBGZFBlockInformationIntegrationTest_testBamFile", ".out");
+        final File expectedOutput = new File(toolsTestDir + "PrintBGZFBlockInformation/expected_PrintBGZFBlockInformationIntegrationTest_testBamFile.out");
+
+        final String[] args = {
+                "--bgzf-file", input.getAbsolutePath(),
+                "--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME, actualOutput.getAbsolutePath()
+        };
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(actualOutput, expectedOutput);
+    }
 }
diff --git a/...intBGZFBlockInformation/expected_PrintBGZFBlockInformationIntegrationTest_testBamFile.out b/...intBGZFBlockInformation/expected_PrintBGZFBlockInformationIntegrationTest_testBamFile.out
@@ -0,0 +1,14 @@
+BGZF block information for file: reads_data_source_test1.bam
+
+Block #1 at file offset 0
+	- compressed size: 380
+	- uncompressed size: 1971
+
+Block #2 at file offset 380
+	- compressed size: 28
+	- uncompressed size: 0
+
+***************************************************************************
+Final BGZF 0-byte terminator block FOUND as expected at block number 2
+***************************************************************************
+