/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ public boolean filterOut(final SAMRecord first, final SAMRecord second) { // only filter out the pair if both first and second reads have all As return (filterOut(first) && filterOut(second)); } }
/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // only filter out the pair if both first and second reads have all As return (filterOut(first) && filterOut(second)); } }
/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // only filter out the pair if both first and second reads have all As return (filterOut(first) && filterOut(second)); } }
/** * Basic positive and negative tests for the PolyANoiseFilter * * @param sequence The sequence to be tested * @param expectedResult The expected result (true is the sequence should match the filter, otherwise false) */ @Test(dataProvider="data") public void testSolexaNoiseFilter(final String testName, final String sequence, final boolean expectedResult) { builder.addUnmappedFragment("testfrag"); final SAMRecord record = builder.iterator().next(); record.setReadString(sequence); Assert.assertEquals(filter.filterOut(record), expectedResult, testName); }