responding to review comments, also added unit test for generateRefer…

…encePairsAgainstDictionary()
broadinstitute · Jul 27, 2022 · 5648af9 · 5648af9
1 parent 7e3e1fc
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diff --git a/src/main/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibility.java b/src/main/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibility.java
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/reference/ReferenceSequenceTable.java b/src/main/java/org/broadinstitute/hellbender/tools/reference/ReferenceSequenceTable.java
@@ -233,7 +233,7 @@ private String getMD5ForRecord(SAMSequenceRecord record, GATKPath referencePath)
      *
      * @return the list of ReferencePairs for every pair of references
      */
-    public List<ReferencePair> generateReferencePairs(){
+    public final List<ReferencePair> generateReferencePairs(){
         List<ReferencePair> referencePairs = new ArrayList<>();
         for(int i = 0; i < references.size(); i++){
             for(int j = i + 1; j < references.size(); j++){
@@ -248,7 +248,7 @@ public List<ReferencePair> generateReferencePairs(){
      *
      * @return the list of ReferencePairs
      */
-    public List<ReferencePair> generateReferencePairs(GATKPath dictionary){
+    public final List<ReferencePair> generateReferencePairsAgainstDictionary(GATKPath dictionary){
         List<ReferencePair> referencePairs = new ArrayList<>();
         for(int i = 0; i < references.size(); i++){
             GATKPath currRef = references.get(i);
@@ -274,7 +274,7 @@ public List<ReferencePair> compareAllReferences(){
      * @return list of ReferencePairs keyed against the provided dictionary with updated status sets
      */
     public List<ReferencePair> compareAgainstKeyReference(GATKPath dictionary){
-        List<ReferencePair> refPairs = generateReferencePairs(dictionary);
+        List<ReferencePair> refPairs = generateReferencePairsAgainstDictionary(dictionary);
         return analyzeTable(refPairs);
     }
 

diff --git a/...broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java b/...broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java
@@ -11,7 +11,7 @@
 
 public class CheckReferenceCompatibilityIntegrationTest extends CommandLineProgramTest {
 
-    private final String COMPARE_REFERENCES_TEST_FILES_DIRECTORY = "src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/";
+    private final String COMPARE_REFERENCES_TEST_FILES_DIRECTORY = toolsTestDir + "/reference/CompareReferences/";
 
     @DataProvider(name = "testReferenceCompatibilityBAMWithMD5sData")
     public Object[][] testReferenceCompatibilityBAMWithMD5sData() {
@@ -97,13 +97,14 @@ public void testReferenceCompatibilityMultipleBAMs() throws IOException {
     public void testReferenceCompatibilityMultipleReferencesBAMWithMD5s() throws IOException {
         final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini.fasta");
         final File ref2 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_1renamed.fasta");
-        final File ref3 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_chr2snp.fasta");
+        final File ref3 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_missingchr1.fasta");
+        final File ref4 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_chr2snp.fasta");
         final File dict = new File(getToolTestDataDir() + "reads_data_source_test1_withmd5s_missingchr1.bam");
         final File output = createTempFile("testReferenceCompatibilityMultipleReferencesWithMD5s", ".table");
         final File expectedOutput = new File(getToolTestDataDir(), "expected.testReferenceCompatibilityMultipleReferencesBAMWithMD5s.table");
 
         final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath(), "-refcomp", ref2.getAbsolutePath(),
-                "-refcomp", ref3.getAbsolutePath(), "-I", dict.getAbsolutePath(), "-O", output.getAbsolutePath()};
+                "-refcomp", ref3.getAbsolutePath(), "-refcomp", ref4.getAbsolutePath(), "-I", dict.getAbsolutePath(), "-O", output.getAbsolutePath()};
         runCommandLine(args);
 
         IntegrationTestSpec.assertEqualTextFiles(output, expectedOutput);
@@ -133,23 +134,27 @@ public void testReferenceCompatibilityMultipleReferencesBAMWithoutMD5s() throws
     public void testReferenceCompatibilityWithoutMD5sMismatch() throws IOException {
         final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_chr2snp.fasta");
         final File dict = new File(getToolTestDataDir() + "reads_data_source_test1_withoutmd5s.bam");
+        final File output = createTempFile("testReferenceCompatibilityVCFWithMD5s", ".table");
+        final File expectedOutput = new File(getToolTestDataDir(), "expected.testReferenceCompatibilityWithoutMD5Mismatch.table");
 
-        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath() , "-I", dict.getAbsolutePath()};
+        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath() , "-I", dict.getAbsolutePath(), "-O", output.getAbsolutePath()};
         runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expectedOutput);
     }
 
-    // TODO: compatibility based on MD5 faulty since MD5s not in sequence dictionary (see ticket #730 "VCFHeader drops sequence dictionary attributes")
-    @Test(enabled = false)
+    // TODO: compatibility based on MD5 faulty since MD5s not in sequence dictionary (https://github.com/samtools/htsjdk/issues/730)
+    @Test
     public void testReferenceCompatibilityVCFWithMD5s() throws IOException {
-        final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_missingchr1.fasta");
-        final File dict = new File(getToolTestDataDir() + "example_variants_withSequenceDict.vcf");
-        //final File output = createTempFile("testReferenceCompatibilityVCFWithMD5s", ".table");
+        final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini.fasta");
+        final File dict = new File(getToolTestDataDir() + "example_variants_withSequenceDict_withmd5.vcf");
+        final File output = createTempFile("testReferenceCompatibilityVCFWithMD5s", ".table");
         final File expectedOutput = new File(getToolTestDataDir(), "expected.testReferenceCompatibilityVCFWithMD5s.table");
 
-        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath() , "-V", dict.getAbsolutePath()/*, "-O", expectedOutput.getAbsolutePath()*/};
+        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath() , "-V", dict.getAbsolutePath(), "-O", output.getAbsolutePath()};
         runCommandLine(args);
 
-        //IntegrationTestSpec.assertEqualTextFiles(output, expectedOutput);
+        IntegrationTestSpec.assertEqualTextFiles(output, expectedOutput);
     }
 
     @DataProvider(name = "testReferenceCompatibilityVCFWithoutMD5sData")
@@ -187,19 +192,15 @@ public void testReferenceCompatibilityVCFWithoutMD5s(File ref1, File dict, File
         IntegrationTestSpec.assertEqualTextFiles(output, expectedOutput);
     }
 
-    // for quick stdout testing
-    @Test(enabled = false)
-    public void testStdOutput() throws IOException{
-        final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini.fasta");
-        final File ref2 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_1renamed.fasta");
-        final File ref3 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_chr2snp.fasta");
-        final File dict = new File(getToolTestDataDir() + "reads_data_source_test1_withmd5s_missingchr1.bam");
-        //final File output = createTempFile("testReferenceCompatibilityMultipleReferencesWithMD5s", ".table");
-        final File expectedOutput = new File(getToolTestDataDir(), "expected.testReferenceCompatibilityMultipleReferencesBAMWithMD5s.table");
+    @Test(expectedExceptions = UserException.BadInput.class)
+    public void testReferenceCompatibilityBAMandVCF() throws IOException {
+        final File ref1 = new File(COMPARE_REFERENCES_TEST_FILES_DIRECTORY + "hg19mini_chr2snp.fasta");
+        final File bam = new File(getToolTestDataDir() + "reads_data_source_test1_withoutmd5s.bam");
+        final File vcf = new File(getToolTestDataDir() + "example_variants_withSequenceDict_withoutmd5s.vcf");
 
-        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath(), "-refcomp", ref2.getAbsolutePath(),
-                "-refcomp", ref3.getAbsolutePath(), "-I", dict.getAbsolutePath(), "-O", expectedOutput.getAbsolutePath()};
+        final String[] args = new String[] {"-refcomp", ref1.getAbsolutePath() , "-I", bam.getAbsolutePath(), "-V", vcf.getAbsolutePath()};
         runCommandLine(args);
     }
 
+
 }
diff --git a/...st/java/org/broadinstitute/hellbender/tools/reference/ReferenceSequenceTableUnitTest.java b/...st/java/org/broadinstitute/hellbender/tools/reference/ReferenceSequenceTableUnitTest.java
@@ -3,6 +3,8 @@
 import htsjdk.samtools.SAMSequenceDictionary;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.engine.GATKPath;
+import org.broadinstitute.hellbender.engine.ReadsDataSource;
+import org.broadinstitute.hellbender.engine.ReadsPathDataSource;
 import org.broadinstitute.hellbender.engine.ReferenceDataSource;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -24,9 +26,11 @@ private ReferenceSequenceTable tableGenerator(List<GATKPath> references, Compare
         return table;
     }
 
-    private ReferenceSequenceTable tableGenerator(List<GATKPath> references){
+    private ReferenceSequenceTable tableGenerator(GATKPath dictionaryPath, SAMSequenceDictionary dictionary, List<GATKPath> references){
         Map<GATKPath, SAMSequenceDictionary> dictionaries = new LinkedHashMap<>();
-        for(GATKPath path : references){
+
+        dictionaries.put(dictionaryPath, dictionary);
+        for (GATKPath path : references) {
             dictionaries.put(path, ReferenceDataSource.of(path.toPath()).getSequenceDictionary());
         }
 
@@ -128,14 +132,39 @@ public Object[][] testGenerateReferencePairsData() {
                 },
         };
     }
-
     @Test(dataProvider = "testGenerateReferencePairsData")
     public void testGenerateReferencePairs(List<GATKPath> references, int expectedPairs){
         ReferenceSequenceTable table = tableGenerator(references, CompareReferences.MD5CalculationMode.USE_DICT);
         List<ReferencePair> pairs = table.generateReferencePairs();
         Assert.assertEquals(pairs.size(), expectedPairs);
     }
 
+    @DataProvider(name = "testGenerateReferencePairsAgainstDictionaryData")
+    public Object[][] testGenerateReferencePairsAgainstDictionaryData() {
+        return new Object[][]{
+                // references, dictionary, expected number of pairs
+                new Object[]{ Arrays.asList(new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta"),
+                        new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta")),
+                        new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibility/reads_data_source_test1_withmd5s.bam"),
+                        2
+                },
+                new Object[]{ Arrays.asList(new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta"),
+                        new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta"),
+                        new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_1renamed.fasta")),
+                        new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibility/reads_data_source_test1_withmd5s.bam"),
+                        3
+                },
+        };
+    }
+    @Test(dataProvider = "testGenerateReferencePairsAgainstDictionaryData")
+    public void testGenerateReferencePairsAgainstDictionary(List<GATKPath> references, GATKPath dictPath, int expectedPairs){
+        ReadsDataSource readsDataSource = new ReadsPathDataSource(dictPath.toPath());
+        SAMSequenceDictionary dictionary = readsDataSource.getSequenceDictionary();
+        ReferenceSequenceTable table = tableGenerator(dictPath, dictionary, references);
+        List<ReferencePair> pairs = table.generateReferencePairsAgainstDictionary(dictPath);
+        Assert.assertEquals(pairs.size(), expectedPairs);
+    }
+
     @DataProvider(name = "testAnalyzeTableTwoRefsData")
     public Object[][] testAnalyzeTableTwoReferencesData(){
         return new Object[][]{

diff --git a/...eckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_exactmatch.table b/...eckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_exactmatch.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withmd5s.bam
-Reference	Compatibility
-hg19mini.fasta	Compatible, the sequence dictionaries exactly match
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE	The sequence dictionaries exactly match
diff --git a/...ReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_notcompatible.table b/...ReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_notcompatible.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withmd5s.bam
-Reference	Compatibility
-hg19mini_missingchr3.fasta	Not compatible. Status: [SUPERSET]. Run CompareReferences tool for more information on reference differences.
+Reference	Compatibility	Summary
+hg19mini_missingchr3.fasta	NOT_COMPATIBLE	Status: [SUPERSET]. Run CompareReferences tool for more information on reference differences.
diff --git a/...e/CheckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_subset.table b/...e/CheckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithMD5s_subset.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withmd5s_missingchr1.bam
-Reference	Compatibility
-hg19mini.fasta	Compatible, the sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini.fasta reference sequence dictionary. Missing sequence(s): [1]
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE_SUBSET	The sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini.fasta reference sequence dictionary. Missing sequence(s): [1]
diff --git a/...ReferenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_compatible.table b/...ReferenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_compatible.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withoutmd5s.bam
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...erenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_notcompatible.table b/...erenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_notcompatible.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withoutmd5s.bam
-Reference	Compatibility
-hg19mini_missingchr3.fasta	Not compatible. Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
+Reference	Compatibility	Summary
+hg19mini_missingchr3.fasta	NOT_COMPATIBLE	Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
diff --git a/...heckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_subset.table b/...heckReferenceCompatibility/expected.testReferenceCompatibilityBAMWithoutMD5s_subset.table
@@ -1,3 +1,3 @@
 #Current Reference: reads_data_source_test1_withoutmd5s_missingchr1.bam
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths present in the sequence dictionaries match, but reads_data_source_test1_withoutmd5s_missingchr1.bam is a subset of hg19mini.fasta. Missing sequence(s): [1]. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE_SUBSET	All sequence names and lengths present in the sequence dictionaries match, but reads_data_source_test1_withoutmd5s_missingchr1.bam is a subset of hg19mini.fasta. Missing sequence(s): [1]. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...renceCompatibility/expected.testReferenceCompatibilityMultipleReferencesBAMWithMD5s.table b/...renceCompatibility/expected.testReferenceCompatibilityMultipleReferencesBAMWithMD5s.table
@@ -1,5 +1,6 @@
 #Current Reference: reads_data_source_test1_withmd5s_missingchr1.bam
-Reference	Compatibility
-hg19mini.fasta	Compatible, the sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini.fasta reference sequence dictionary. Missing sequence(s): [1]
-hg19mini_1renamed.fasta	Compatible, the sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini_1renamed.fasta reference sequence dictionary. Missing sequence(s): [chr1]
-hg19mini_chr2snp.fasta	Not compatible. Status: [DIFFER_IN_SEQUENCE, DIFFER_IN_SEQUENCES_PRESENT]. Run CompareReferences tool for more information on reference differences.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE_SUBSET	The sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini.fasta reference sequence dictionary. Missing sequence(s): [1]
+hg19mini_1renamed.fasta	COMPATIBLE_SUBSET	The sequence dictionary in reads_data_source_test1_withmd5s_missingchr1.bam is a subset of the hg19mini_1renamed.fasta reference sequence dictionary. Missing sequence(s): [chr1]
+hg19mini_missingchr1.fasta	COMPATIBLE	The sequence dictionaries exactly match
+hg19mini_chr2snp.fasta	NOT_COMPATIBLE	Status: [DIFFER_IN_SEQUENCE, DIFFER_IN_SEQUENCES_PRESENT]. Run CompareReferences tool for more information on reference differences.
diff --git a/...ceCompatibility/expected.testReferenceCompatibilityMultipleReferencesBAMWithoutMD5s.table b/...ceCompatibility/expected.testReferenceCompatibilityMultipleReferencesBAMWithoutMD5s.table
@@ -1,5 +1,5 @@
 #Current Reference: reads_data_source_test1_withoutmd5s.bam
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
-hg19mini_1renamed.fasta	Not compatible. Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
-hg19mini_chr2snp.fasta	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+hg19mini_1renamed.fasta	NOT_COMPATIBLE	Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
+hg19mini_chr2snp.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...eference/CheckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithMD5s.table b/...eference/CheckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithMD5s.table
@@ -1,3 +1,3 @@
-#Current Reference: example_variants_withSequenceDict.vcf
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+#Current Reference: example_variants_withSequenceDict_withmd5.vcf
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...CheckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_match.table b/...CheckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_match.table
@@ -1,3 +1,3 @@
 #Current Reference: example_variants_withSequenceDict_withoutmd5s.vcf
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...erenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_notcompatible.table b/...erenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_notcompatible.table
@@ -1,3 +1,3 @@
 #Current Reference: example_variants_withSequenceDict_withoutmd5s.vcf
-Reference	Compatibility
-hg19mini_missingchr3.fasta	Not compatible. Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
+Reference	Compatibility	Summary
+hg19mini_missingchr3.fasta	NOT_COMPATIBLE	Status: COMMON_SUBSET. Run CompareReferences tool for more information on reference differences.
diff --git a/...heckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_subset.table b/...heckReferenceCompatibility/expected.testReferenceCompatibilityVCFWithoutMD5s_subset.table
@@ -1,3 +1,3 @@
 #Current Reference: example_variants_withSequenceDict_withoutmd5s_missingchr1.vcf
-Reference	Compatibility
-hg19mini.fasta	All sequence names and lengths present in the sequence dictionaries match, but example_variants_withSequenceDict_withoutmd5s_missingchr1.vcf is a subset of hg19mini.fasta. Missing sequence(s): [1]. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
+Reference	Compatibility	Summary
+hg19mini.fasta	COMPATIBLE_SUBSET	All sequence names and lengths present in the sequence dictionaries match, but example_variants_withSequenceDict_withoutmd5s_missingchr1.vcf is a subset of hg19mini.fasta. Missing sequence(s): [1]. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.
diff --git a/...e/CheckReferenceCompatibility/expected.testReferenceCompatibilityWithoutMD5Mismatch.table b/...e/CheckReferenceCompatibility/expected.testReferenceCompatibilityWithoutMD5Mismatch.table
@@ -0,0 +1,3 @@
+#Current Reference: reads_data_source_test1_withoutmd5s.bam
+Reference	Compatibility	Summary
+hg19mini_chr2snp.fasta	COMPATIBLE	All sequence names and lengths match in the sequence dictionaries. Since the MD5s are lacking, we can't confirm there aren't mismatching bases in the references.