Package picard.sam.markduplicates.util

Examples of picard.sam.markduplicates.util.OpticalDuplicateFinder

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public class OpticalDuplicateFinderTest {

    /** Tests rapidParseInt for positive and negative numbers, as well as non-digit suffixes */
    @Test
    public void testRapidParseInt() {
        final OpticalDuplicateFinder opticalDuplicateFinder = new OpticalDuplicateFinder();
        for (int i = -100; i < 100; i++) {
            Assert.assertEquals(opticalDuplicateFinder.rapidParseInt(Integer.toString(i)), i);

            // trailing characters
            Assert.assertEquals(opticalDuplicateFinder.rapidParseInt(Integer.toString(i)+"A"), i);
            Assert.assertEquals(opticalDuplicateFinder.rapidParseInt(Integer.toString(i)+"ACGT"), i);
            Assert.assertEquals(opticalDuplicateFinder.rapidParseInt(Integer.toString(i)+".1"), i);
        }
    }
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    }

    /** Tests that we split the string early, with the correct # of fields, and modified values */
    @Test
    public void testGetRapidDefaultReadNameRegexSplit() {
        final OpticalDuplicateFinder opticalDuplicateFinder = new OpticalDuplicateFinder();
        for (int i = 1; i < 10; i++) {
            doTestGetRapidDefaultReadNameRegexSplit((i <= 5) ? i : 5, opticalDuplicateFinder);
        }
    }
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    }

    // NB: these tests fails due to overflow in the duplicate finder test.  This has been the behavior previously, so keep it for now.
    @Test(dataProvider = "testParseReadNameDataProvider", enabled = false)
    public void testParseReadName(final String readName, final int tile, final int x, final int y) {
        OpticalDuplicateFinder opticalDuplicateFinder = new OpticalDuplicateFinder();
        OpticalDuplicateFinder.PhysicalLocation loc = new ReadEndsForMarkDuplicates();
        Assert.assertTrue(opticalDuplicateFinder.addLocationInformation(readName, loc));
        Assert.assertEquals(loc.getTile(), tile);
        Assert.assertEquals(loc.getX(), x);
        Assert.assertEquals(loc.getY(), y);
    }
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Related Classes of picard.sam.markduplicates.util.OpticalDuplicateFinder

  • picard.sam.markduplicates.util.OpticalDuplicateFinderTest
  • java.util.regex.Matcher
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