adding new ReadQueryNameComparator (#4731)

* added a new queryname comparator for GATKRead it operates on GATKRead instead of SAMRecord
* this matches the results of SAMRecordQueryNameComparator exactly

src/main/java/org/broadinstitute/hellbender/utils/read/ReadQueryNameComparator.java

@@ -0,0 +1,61 @@
+package org.broadinstitute.hellbender.utils.read;
+
+import htsjdk.samtools.SAMRecordQueryNameComparator;
+import htsjdk.samtools.SAMTag;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+/**
+ * compare {@link GATKRead} by queryname
+ * duplicates the exact ordering of {@link SAMRecordQueryNameComparator}
+ */
+public class ReadQueryNameComparator implements Comparator<GATKRead>, Serializable {
+    private static final long serialVersionUID = 1L;
+
+    @Override
+    public int compare(final GATKRead read1, final GATKRead read2) {
+        int cmp = compareReadNames(read1, read2);
+        if (cmp != 0) {
+            return cmp;
+        }
+
+        final boolean r1Paired = read1.isPaired();
+        final boolean r2Paired = read2.isPaired();
+
+        if (r1Paired || r2Paired) {
+            if (!r1Paired) return 1;
+            else if (!r2Paired) return -1;
+            else if (read1.isFirstOfPair()  && read2.isSecondOfPair()) return -1;
+            else if (read1.isSecondOfPair() && read2.isFirstOfPair()) return 1;
+        }
+
+        if (read1.isReverseStrand() != read2.isReverseStrand()) {
+            return (read1.isReverseStrand()? 1: -1);
+        }
+        if (read1.isSecondaryAlignment() != read2.isSecondaryAlignment()) {
+            return read2.isSecondaryAlignment()? -1: 1;
+        }
+        if (read1.isSupplementaryAlignment() != read2.isSupplementaryAlignment()) {
+            return read2.isSupplementaryAlignment() ? -1 : 1;
+        }
+        final Integer hitIndex1 = read1.getAttributeAsInteger(SAMTag.HI.name());
+        final Integer hitIndex2 = read2.getAttributeAsInteger(SAMTag.HI.name());
+        if (hitIndex1 != null) {
+            if (hitIndex2 == null) return 1;
+            else {
+                cmp = hitIndex1.compareTo(hitIndex2);
+                if (cmp != 0) return cmp;
+            }
+        } else if (hitIndex2 != null) return -1;
+        return 0;
+    }
+
+    /**
+     * compare read names lexicographically without any additional tie breakers
+     */
+    public int compareReadNames(final GATKRead read1, final GATKRead read2) {
+        return read1.getName().compareTo(read2.getName());
+    }
+}
+

src/test/java/org/broadinstitute/hellbender/utils/read/ReadQueryNameComparatorUnitTest.java

@@ -0,0 +1,134 @@
+package org.broadinstitute.hellbender.utils.read;
+
+import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMRecordQueryNameComparator;
+import htsjdk.samtools.SAMTag;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.engine.ReadsDataSource;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+import java.util.*;
+
+
+public class ReadQueryNameComparatorUnitTest extends GATKBaseTest {
+
+    public static final SAMFileHeader HEADER =ArtificialReadUtils.createArtificialSamHeader();
+    public static final String NAME = "NAME";
+
+    /**
+     * Tests that the ordering produced by {@link ReadQueryNameComparator} matches queryname ordering
+     * as produced by htsjdk's {@link SAMRecordQueryNameComparator} for a representative selection of reads. Ignores
+     * differences in tie-breaking done for reads with the same position -- just asserts that the reads are
+     * queryname-sorted according to htsjdk, including unmapped reads with and without an assigned position.
+     */
+    @Test
+    public void testComparatorOrderingMatchesHtsjdkFileOrdering() throws IOException {
+        final String inputBam = publicTestDir + "org/broadinstitute/hellbender/utils/read/comparator_test_with_unmapped.bam";
+        final List<GATKRead> reads = new ArrayList<>();
+        SAMFileHeader header;
+
+        try ( final ReadsDataSource readsSource = new ReadsDataSource(IOUtils.getPath(inputBam)) ) {
+            header = readsSource.getHeader();
+
+            for ( GATKRead read : readsSource ) {
+                reads.add(read);
+            }
+        }
+
+        // Randomize ordering and then re-sort
+        Collections.shuffle(reads);
+        reads.sort(new ReadQueryNameComparator());
+
+        final SAMRecordQueryNameComparator samComparator = new SAMRecordQueryNameComparator();
+        GATKRead previousRead = null;
+        for ( final GATKRead currentRead : reads ) {
+            if ( previousRead != null ) {
+                Assert.assertTrue(samComparator.compare(previousRead.convertToSAMRecord(header), currentRead.convertToSAMRecord(header)) <= 0,
+                                  "Reads are out of order: " + previousRead + " and " + currentRead);
+            }
+            previousRead = currentRead;
+        }
+    }
+
+    @DataProvider
+    public Object[][] getNames(){
+        return new Object[][]{
+                {"A", "B", -1},
+                {"A","A", 0},
+                {"AA", "A", 1},
+                {"1","10", -1},
+                {"2", "10", 1}
+        };
+    }
+
+
+
+    @Test(dataProvider = "getNames")
+    public void testCompareNames(String firstName, String secondName, int expected) throws Exception {
+        ReadQueryNameComparator comp = new ReadQueryNameComparator();
+        GATKRead first = getRead(firstName);
+        GATKRead second = getRead(secondName);
+        Assert.assertEquals(comp.compareReadNames(first, second ), expected);
+        Assert.assertEquals(comp.compareReadNames(second, first), -expected);
+        Assert.assertEquals(comp.compareReadNames(first, first), 0);
+        Assert.assertEquals(comp.compareReadNames(second, second), 0);
+    }
+
+    private static GATKRead getRead(String firstName) {
+        final GATKRead read = ArtificialReadUtils.createArtificialRead(HEADER, firstName, 1, 100, 10);
+        return read;
+    }
+
+    @DataProvider
+    public Iterator<Object[]> getReads(){
+        final GATKRead differentName = getRead(NAME+NAME);
+
+        final GATKRead unpaired = getRead(NAME);
+        unpaired.setIsPaired(false);
+
+        final GATKRead paired = getRead(NAME);
+        paired.setIsPaired(true);
+
+        final GATKRead firstOfPair = getRead(NAME);
+        firstOfPair.setIsFirstOfPair();
+
+        final GATKRead secondOfPair = getRead(NAME);
+        secondOfPair.setIsSecondOfPair();
+
+        final GATKRead reverseStrand = getRead(NAME);
+        reverseStrand.setIsReverseStrand(true);
+
+        final GATKRead supplementary = getRead(NAME);
+        supplementary.setIsSupplementaryAlignment(true);
+
+        final GATKRead secondary = getRead(NAME);
+        secondary.setIsSecondaryAlignment(true);
+
+        final GATKRead tagHI1 = getRead(NAME);
+        tagHI1.setAttribute(SAMTag.HI.name(), 1);
+
+        final GATKRead tagHI2 = getRead(NAME);
+        tagHI2.setAttribute(SAMTag.HI.name(), 2);
+
+        List<GATKRead> reads = Arrays.asList(differentName, unpaired, paired, firstOfPair, secondOfPair, reverseStrand, supplementary, secondary, tagHI1, tagHI2);
+        List<Object[]> tests = new ArrayList<>();
+        for(GATKRead left: reads){
+            for(GATKRead right: reads){
+                tests.add(new Object[]{left, right});
+            }
+        };
+        return tests.iterator();
+    }
+
+    @Test(dataProvider = "getReads")
+    public void testTieBreakers(GATKRead left, GATKRead right){
+        ReadQueryNameComparator readComparator = new ReadQueryNameComparator();
+        SAMRecordQueryNameComparator samComparator = new SAMRecordQueryNameComparator();
+        Assert.assertEquals(readComparator.compare(left, right), samComparator.compare(left.convertToSAMRecord(HEADER), right.convertToSAMRecord(HEADER)));
+    }
+
+}