Revert "- Expand SamLocusAndReferenceIterator tests to cover BAMs and…

… CRAMs." This reverts commit 651bd0c.
samtools · Dec 17, 2020 · 2c4c9b2 · 2c4c9b2
1 parent 651bd0c
commit 2c4c9b2
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Showing 4 changed files with 24 additions and 164 deletions.
diff --git a/src/main/java/htsjdk/samtools/reference/SamLocusAndReferenceIterator.java b/src/main/java/htsjdk/samtools/reference/SamLocusAndReferenceIterator.java
@@ -29,8 +29,7 @@
 
 import java.util.List;
 
-import static htsjdk.samtools.util.SamLocusIterator.LocusInfo;
-import static htsjdk.samtools.util.SamLocusIterator.RecordAndOffset;
+import static htsjdk.samtools.util.SamLocusIterator.*;
 
 /**
  * Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.

diff --git a/src/main/java/htsjdk/variant/vcf/SamFileUtils.java b/src/main/java/htsjdk/variant/vcf/SamFileUtils.java
diff --git a/src/test/java/htsjdk/samtools/reference/SamLocusAndReferenceIteratorTest.java b/src/test/java/htsjdk/samtools/reference/SamLocusAndReferenceIteratorTest.java
@@ -1,87 +1,26 @@
 package htsjdk.samtools.reference;
 
 import htsjdk.HtsjdkTest;
-import htsjdk.samtools.SAMFileWriter;
-import htsjdk.samtools.SAMFileWriterFactory;
-import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
-import htsjdk.samtools.util.Interval;
-import htsjdk.samtools.util.IntervalList;
-import htsjdk.samtools.util.OverlapDetector;
-import htsjdk.samtools.util.SamLocusIterator;
-import htsjdk.samtools.util.SequenceUtil;
-import htsjdk.variant.vcf.SamFileUtils;
+import htsjdk.samtools.util.*;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.io.IOException;
 
 public class SamLocusAndReferenceIteratorTest extends HtsjdkTest {
     static private final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools/reference");
 
-    final File referenceAssembly18_trimmed = new File(TEST_DATA_DIR, "Homo_sapiens_assembly18.trimmed.fasta");
-    final File referenceWithTrailingNewWhiteSpace = new File(TEST_DATA_DIR, "reference_with_trailing_whitespace.fasta");
+    @Test
+    public void testSamLocusAndReferenceIterator() {
 
-    File simpleSmallFileCram;
-    File simpleSmallFileSam;
-    File simpleSmallFileBam;
-
-    File leadingInsertionCram;
-    File leadingInsertionSam;
-    File leadingInsertionBam;
-
-    @DataProvider
-    Object[][] testSamLocusAndReferenceIteratorData() {
-        return new Object[][]{
-                {simpleSmallFileSam, false},
-                {simpleSmallFileBam, false},
-                {simpleSmallFileCram, true}
-        };
-    }
-
-    @BeforeSuite
-    void setup() throws IOException {
-
-        simpleSmallFileSam = new File(TEST_DATA_DIR, "simpleSmallFile.sam");
-        leadingInsertionSam = new File(TEST_DATA_DIR, "leading_insertion.sam");
-
-        simpleSmallFileCram = createTemporarySamFileFromInput(simpleSmallFileSam, "SamLocusAndReferenceIteratorTest", ".cram", referenceAssembly18_trimmed);
-        leadingInsertionCram = createTemporarySamFileFromInput(leadingInsertionSam, "SamLocusAndReferenceIteratorTest", ".cram", referenceAssembly18_trimmed);
-
-        simpleSmallFileBam = createTemporarySamFileFromInput(simpleSmallFileSam, "SamLocusAndReferenceIteratorTest", ".bam", referenceAssembly18_trimmed);
-        leadingInsertionBam = createTemporarySamFileFromInput(leadingInsertionSam, "SamLocusAndReferenceIteratorTest", ".bam", referenceAssembly18_trimmed);
-
-    }
-
-    public static File createTemporarySamFileFromInput(final File samFile, final String tempFilePrefix, final String suffix, final File reference) throws IOException {
-
-        final File output = SamFileUtils.createTemporaryIndexedFile(tempFilePrefix, suffix);
-
-        try (final SamReader in = SamReaderFactory.makeDefault().open(samFile);
-             final SAMFileWriter out = new SAMFileWriterFactory().makeWriter(in.getFileHeader().clone(), true, output, reference)) {
-            for (final SAMRecord record : in) {
-                out.addAlignment(record);
-            }
-        }
-        return output;
-    }
-
-
-    @Test(dataProvider = "testSamLocusAndReferenceIteratorData")
-    public void testSamLocusAndReferenceIterator(final File samFile, boolean readerNeedsReference) {
-
-        final ReferenceSequenceFile referenceSequenceFile = new FastaSequenceFile(referenceAssembly18_trimmed, false);
+        final File reference = new File(TEST_DATA_DIR, "Homo_sapiens_assembly18.trimmed.fasta");
+        final File samFile = new File(TEST_DATA_DIR, "simpleSmallFile.sam");
+        final ReferenceSequenceFile referenceSequenceFile = new FastaSequenceFile(reference, false);
         final ReferenceSequenceFileWalker referenceSequenceFileWalker = new ReferenceSequenceFileWalker(referenceSequenceFile);
 
-        final SamReaderFactory samReaderFactory = SamReaderFactory.makeDefault();
-        if (readerNeedsReference) {
-            samReaderFactory.referenceSequence(referenceAssembly18_trimmed);
-        }
-        final SamReader samReader = samReaderFactory.open(samFile);
+        final SamReader samReader = SamReaderFactory.makeDefault().open(samFile);
         final SamLocusIterator samLocusIterator = new SamLocusIterator(samReader);
         final SamLocusAndReferenceIterator samLocusAndReferences = new SamLocusAndReferenceIterator(referenceSequenceFileWalker, samLocusIterator);
 
@@ -93,53 +32,36 @@ public void testSamLocusAndReferenceIterator(final File samFile, boolean readerN
         overlapDetector.addAll(intervalList.getIntervals(), intervalList.getIntervals());
 
         for (final SamLocusAndReferenceIterator.SAMLocusAndReference samLocusAndReference : samLocusAndReferences) {
-            // The sam file only has coverage in the intervals that are within 'intervalList', and there the coverage should
-            // be exactly 2 since there are two overlapping, paired reads. This is what this test is testing:
+        // The sam file only has coverage in the intervals that are within 'intervalList', and there the coverage should
+        // be exactly 2 since there are two overlapping, paired reads. This is what this test is testing:
             Assert.assertEquals(samLocusAndReference.getRecordAndOffsets().size(), overlapDetector.overlapsAny(samLocusAndReference.getLocus()) ? 2 : 0, "Position:" + samLocusAndReference.getLocus().toString());
 
             // all the reads are equal to the reference...this is what this test is testing.
-            for (final SamLocusIterator.RecordAndOffset recordAndOffset : samLocusAndReference.getRecordAndOffsets()) {
+            for (final SamLocusIterator.RecordAndOffset recordAndOffset : samLocusAndReference.getRecordAndOffsets())
                 Assert.assertTrue(SequenceUtil.basesEqual(samLocusAndReference.getReferenceBase(), recordAndOffset.getReadBase()), "Record: " + recordAndOffset.getRecord() + " Position:" + samLocusAndReference.getLocus().toString());
-            }
         }
     }
 
-    @Test(dataProvider = "testSamLocusAndReferenceIteratorData", expectedExceptions = IllegalArgumentException.class)
-    public void testSamLocusAndReferenceIteratorMismatch(final File samFile, boolean readerNeedsReference) {
-        final File reference = referenceWithTrailingNewWhiteSpace;
+    @Test(expectedExceptions = IllegalArgumentException.class)
+    public void testSamLocusAndReferenceIteratorMismatch() {
+        final File reference = new File(TEST_DATA_DIR, "reference_with_trailing_whitespace.fasta");
+        final File samFile = new File(TEST_DATA_DIR, "simpleSmallFile.sam");
         final ReferenceSequenceFile referenceSequenceFile = new FastaSequenceFile(reference, false);
         final ReferenceSequenceFileWalker referenceSequenceFileWalker = new ReferenceSequenceFileWalker(referenceSequenceFile);
 
-        final SamReaderFactory samReaderFactory = SamReaderFactory.makeDefault();
-        if (readerNeedsReference) {
-            samReaderFactory.referenceSequence(reference);
-        }
-        final SamReader samReader = samReaderFactory.open(samFile);
+        final SamReader samReader = SamReaderFactory.makeDefault().open(samFile);
         final SamLocusIterator samLocusIterator = new SamLocusIterator(samReader);
         new SamLocusAndReferenceIterator(referenceSequenceFileWalker, samLocusIterator); // should throw
     }
 
-
-    @DataProvider
-    Object[][] testSamLocusAndReferenceIteratorLeadingInsertionData() {
-        return new Object[][]{
-                {leadingInsertionSam, false},
-                {leadingInsertionBam, false},
-                {leadingInsertionCram, true}
-        };
-    }
-
-    @Test(dataProvider = "testSamLocusAndReferenceIteratorLeadingInsertionData")
-    public void testSamLocusAndReferenceIteratorLeadingInsertion(final File samFile, boolean readerNeedsReference) {
-        final File reference = referenceAssembly18_trimmed;
+    @Test
+    public void testSamLocusAndReferenceIteratorLeadingInsertion() {
+        final File reference = new File(TEST_DATA_DIR, "Homo_sapiens_assembly18.trimmed.fasta");
+        final File samFile = new File(TEST_DATA_DIR, "leading_insertion.sam");
         final ReferenceSequenceFile referenceSequenceFile = new FastaSequenceFile(reference, false);
         final ReferenceSequenceFileWalker referenceSequenceFileWalker = new ReferenceSequenceFileWalker(referenceSequenceFile);
 
-        final SamReaderFactory samReaderFactory = SamReaderFactory.makeDefault();
-        if (readerNeedsReference) {
-            samReaderFactory.referenceSequence(reference);
-        }
-        final SamReader samReader = samReaderFactory.open(samFile);
+        final SamReader samReader = SamReaderFactory.makeDefault().open(samFile);
         final SamLocusIterator samLocusIterator = new SamLocusIterator(samReader);
         samLocusIterator.setIncludeIndels(true);
         final SamLocusAndReferenceIterator samLocusAndReferences = new SamLocusAndReferenceIterator(referenceSequenceFileWalker, samLocusIterator);
@@ -170,7 +92,8 @@ public void testSamLocusAndReferenceIteratorLeadingInsertion(final File samFile,
 
             if (overlapDetector.overlapsAny(samLocusAndReference.getLocus())) {
                 Assert.assertEquals(samLocusAndReference.getRecordAndOffsets().size(), 2);
-            } else {
+            }
+            else {
                 Assert.assertEquals(samLocusAndReference.getRecordAndOffsets().size(), 0);
             }
         }

diff --git a/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java b/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java
@@ -812,4 +812,5 @@ public void testOverlappingGappedAlignmentsWithIndels() {
             ++i;
         }
     }
+
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -812,4 +812,5 @@ public void testOverlappingGappedAlignmentsWithIndels() { @@
                 ++i;
             }
         }
     }