Add a samtools roundtrip test that fails without this change.

samtools · Apr 10, 2024 · bf67f68 · bf67f68
1 parent 2d5b20f
commit bf67f68
Showing 1 changed file with 33 additions and 10 deletions.
diff --git a/src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java b/src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java
@@ -25,28 +25,40 @@ public class CRAMAllEncodingStrategiesTest extends HtsjdkTest {
  public Object[][] roundTripTestFiles() {
  return new Object[][] {
  { new File(TEST_DATA_DIR, "NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram"),
- new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta") },
+ new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"),
+ false, false },
+ // use lenient equality to only test read names, bases and qual scores
+ { new File(TEST_DATA_DIR, "mitoAlignmentStartTestGATKGen.cram"),
+ new File(TEST_DATA_DIR, "mitoAlignmentStartTest.fa"), true, false }
  };
  }
 
  @Test(dataProvider = "roundTripTestFiles")
- public final void testRoundTripDefaultEncodingStrategy(final File sourceFile, final File referenceFile) throws IOException {
+ public final void testRoundTripDefaultEncodingStrategy(
+ final File sourceFile,
+ final File referenceFile,
+ final boolean lenientEquality,
+ final boolean emitDetail) throws IOException {
  final CRAMEncodingStrategy testStrategy = new CRAMEncodingStrategy();
  final File tempOutCRAM = File.createTempFile("testRoundTrip", ".cram");
  tempOutCRAM.deleteOnExit();
  CRAMTestUtils.writeToCRAMWithEncodingStrategy(testStrategy, sourceFile, tempOutCRAM, referenceFile);
- assertRoundTripFidelity(sourceFile, tempOutCRAM, referenceFile, false);
- assertRoundtripFidelityWithSamtools(tempOutCRAM, referenceFile);
+ assertRoundTripFidelity(sourceFile, tempOutCRAM, referenceFile, lenientEquality, emitDetail);
+ assertRoundtripFidelityWithSamtools(tempOutCRAM, referenceFile, lenientEquality, emitDetail);
  }
 
  @Test(dataProvider = "roundTripTestFiles")
- public final void testAllEncodingStrategyCombinations(final File cramSourceFile, final File referenceFile) throws IOException {
+ public final void testAllEncodingStrategyCombinations(
+ final File cramSourceFile,
+ final File referenceFile,
+ final boolean lenientEquality,
+ final boolean emitDetail) throws IOException {
  for (final Tuple<String, CRAMEncodingStrategy> testStrategy : getAllEncodingStrategies()) {
  final File tempOutCRAM = File.createTempFile("allEncodingStrategyCombinations", ".cram");
  tempOutCRAM.deleteOnExit();
  CRAMTestUtils.writeToCRAMWithEncodingStrategy(testStrategy.b, cramSourceFile, tempOutCRAM, referenceFile);
- assertRoundTripFidelity(cramSourceFile, tempOutCRAM, referenceFile, false);
- assertRoundtripFidelityWithSamtools(tempOutCRAM, referenceFile);
+ assertRoundTripFidelity(cramSourceFile, tempOutCRAM, referenceFile, lenientEquality, emitDetail);
+ assertRoundtripFidelityWithSamtools(tempOutCRAM, referenceFile, lenientEquality, emitDetail);
  }
  }
 
@@ -82,6 +94,7 @@ public void assertRoundTripFidelity(
  final File sourceFile,
  final File targetCRAMFile,
  final File referenceFile,
+ final boolean lenientEquality,
  final boolean emitDetail) throws IOException {
  try (final SamReader sourceReader = SamReaderFactory.makeDefault()
  .referenceSequence(referenceFile)
@@ -91,7 +104,13 @@ public void assertRoundTripFidelity(
  final SAMRecordIterator sourceIterator = sourceReader.iterator();
  final SAMRecordIterator targetIterator = copyReader.getIterator();
  while (sourceIterator.hasNext() && targetIterator.hasNext()) {
- if (emitDetail) {
+ if (lenientEquality) {
+ final SAMRecord sourceRec = sourceIterator.next();
+ final SAMRecord targetRec = targetIterator.next();
+ Assert.assertEquals(targetRec.getReadName(), sourceRec.getReadName());
+ Assert.assertEquals(targetRec.getReadBases(), sourceRec.getReadBases());
+ Assert.assertEquals(targetRec.getBaseQualities(), sourceRec.getBaseQualities());
+ } else if (emitDetail) {
  final SAMRecord sourceRec = sourceIterator.next();
  final SAMRecord targetRec = targetIterator.next();
  if (!sourceRec.equals(targetRec)) {
@@ -108,13 +127,17 @@ public void assertRoundTripFidelity(
  }
  }
 
- private void assertRoundtripFidelityWithSamtools(final File sourceCRAM, final File referenceFile) throws IOException {
+ private void assertRoundtripFidelityWithSamtools(
+ final File sourceCRAM,
+ final File referenceFile,
+ final boolean lenientEquality,
+ final boolean emitDetail) throws IOException {
  if (SamtoolsTestUtils.isSamtoolsAvailable()) {
  final File samtoolsOutFile = SamtoolsTestUtils.convertToCRAM(
  sourceCRAM,
  referenceFile,
  "--input-fmt-option decode_md=0 --output-fmt-option store_md=0 --output-fmt-option store_nm=0");
- assertRoundTripFidelity(sourceCRAM, samtoolsOutFile, referenceFile, false);
+ assertRoundTripFidelity(sourceCRAM, samtoolsOutFile, referenceFile, lenientEquality, emitDetail);
  }
  }